HEADER SUGAR BINDING PROTEIN 01-FEB-23 8I7Q TITLE COBALT AND CALCIUM COORDINATED CONCANAVALIN A AT PH 7.4 FROM CANAVALIA TITLE 2 ENSIFORMIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONCANAVALIN A; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANAVALIA ENSIFORMIS; SOURCE 3 ORGANISM_TAXID: 3823 KEYWDS LECTIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.HWANG,J.H.JEONG,S.J.LEE REVDAT 2 17-JAN-24 8I7Q 1 JRNL REVDAT 1 27-DEC-23 8I7Q 0 JRNL AUTH Y.HWANG,J.H.JEONG,D.H.LEE,S.J.LEE JRNL TITL SELECTIVE INTERACTIONS OF CO 2+ -CA 2+ -CONCANAVALIN A WITH JRNL TITL 2 HIGH MANNOSE N -GLYCANS. JRNL REF DALTON TRANS V. 53 428 2024 JRNL REFN ESSN 1477-9234 JRNL PMID 38086668 JRNL DOI 10.1039/D3DT03575A REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 5883 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.262 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 585 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 27.9300 - 4.4900 1.00 1383 154 0.2231 0.2593 REMARK 3 2 4.4900 - 3.5700 1.00 1314 149 0.2456 0.2831 REMARK 3 3 3.5600 - 3.1100 1.00 1297 138 0.2898 0.3457 REMARK 3 4 3.1100 - 2.8300 0.99 1304 144 0.3718 0.4076 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.540 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 : 0.004 1851 REMARK 3 ANGLE : 0.811 2524 REMARK 3 CHIRALITY : 0.051 290 REMARK 3 PLANARITY : 0.005 326 REMARK 3 DIHEDRAL : 13.165 250 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 8I7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300034920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : IN-VACUUM UNDULATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5904 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.830 REMARK 200 RESOLUTION RANGE LOW (A) : 27.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M COBALT(II) CHLORIDE REMARK 280 HEXAHYDRATE, 0.1 M MES MONOHYDRATE PH 6.5, 1.8 M AMMONIUM REMARK 280 SULFATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.91000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.02500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.30000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.91000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.02500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.30000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.91000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.02500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.30000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.91000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.02500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.30000 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 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 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 ARG A 33 87.58 -68.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 301 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 8 OE2 REMARK 620 2 ASP A 10 OD2 115.2 REMARK 620 3 ASP A 19 OD1 148.6 95.6 REMARK 620 4 HIS A 24 NE2 95.9 89.3 89.9 REMARK 620 5 HOH A 405 O 78.2 89.6 97.3 172.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 ASP A 10 OD2 54.8 REMARK 620 3 TYR A 12 O 76.5 110.4 REMARK 620 4 ASN A 14 OD1 147.2 156.4 78.2 REMARK 620 5 ASP A 19 OD2 116.9 69.2 100.6 87.9 REMARK 620 6 HOH A 407 O 104.4 76.6 171.1 97.6 86.9 REMARK 620 N 1 2 3 4 5 DBREF 8I7Q A 1 237 PDB 8I7Q 8I7Q 1 237 SEQRES 1 A 237 ALA ASP THR ILE VAL ALA VAL GLU LEU ASP THR TYR PRO SEQRES 2 A 237 ASN THR ASP ILE GLY ASP PRO SER TYR PRO HIS ILE GLY SEQRES 3 A 237 ILE ASP ILE LYS SER VAL ARG SER LYS LYS THR ALA LYS SEQRES 4 A 237 TRP ASN MET GLN ASN GLY LYS VAL GLY THR ALA HIS ILE SEQRES 5 A 237 ILE TYR ASN SER VAL GLY LYS ARG LEU SER ALA VAL VAL SEQRES 6 A 237 SER TYR PRO ASN GLY ASP SER ALA THR VAL SER TYR ASP SEQRES 7 A 237 VAL ASP LEU ASP ASN VAL LEU PRO GLU TRP VAL ARG VAL SEQRES 8 A 237 GLY LEU SER ALA SER THR GLY LEU TYR LYS GLU THR ASN SEQRES 9 A 237 THR ILE LEU SER TRP SER PHE THR SER LYS LEU LYS SER SEQRES 10 A 237 ASN SER THR HIS GLU THR ASN ALA LEU HIS PHE MET PHE SEQRES 11 A 237 ASN GLN PHE SER LYS ASP GLN LYS ASP LEU ILE LEU GLN SEQRES 12 A 237 GLY ASP ALA THR THR GLY THR GLU GLY ASN LEU ARG LEU SEQRES 13 A 237 THR ARG VAL SER SER ASN GLY SER PRO GLN GLY SER SER SEQRES 14 A 237 VAL GLY ARG ALA LEU PHE TYR ALA PRO VAL HIS ILE TRP SEQRES 15 A 237 GLU SER SER ALA VAL VAL ALA SER PHE GLU ALA THR PHE SEQRES 16 A 237 THR PHE LEU ILE LYS SER PRO ASP SER HIS PRO ALA ASP SEQRES 17 A 237 GLY ILE ALA PHE PHE ILE SER ASN ILE ASP SER SER ILE SEQRES 18 A 237 PRO SER GLY SER THR GLY ARG LEU LEU GLY LEU PHE PRO SEQRES 19 A 237 ASP ALA ASN HET CO A 301 1 HET CA A 302 1 HETNAM CO COBALT (II) ION HETNAM CA CALCIUM ION FORMUL 2 CO CO 2+ FORMUL 3 CA CA 2+ FORMUL 4 HOH *19(H2 O) HELIX 1 AA1 ASN A 14 GLY A 18 5 5 HELIX 2 AA2 ASP A 80 VAL A 84 5 5 HELIX 3 AA3 THR A 150 GLY A 152 5 3 SHEET 1 AA1 7 LYS A 36 LYS A 39 0 SHEET 2 AA1 7 HIS A 24 ILE A 29 -1 N ILE A 25 O ALA A 38 SHEET 3 AA1 7 ILE A 4 ASP A 10 -1 N ALA A 6 O ASP A 28 SHEET 4 AA1 7 GLY A 209 ASN A 216 -1 O ILE A 210 N LEU A 9 SHEET 5 AA1 7 TRP A 88 THR A 97 -1 N SER A 94 O ALA A 211 SHEET 6 AA1 7 SER A 169 PHE A 175 -1 O PHE A 175 N VAL A 91 SHEET 7 AA1 7 LEU A 140 GLY A 144 -1 N ILE A 141 O LEU A 174 SHEET 1 AA2 6 LYS A 36 LYS A 39 0 SHEET 2 AA2 6 HIS A 24 ILE A 29 -1 N ILE A 25 O ALA A 38 SHEET 3 AA2 6 ILE A 4 ASP A 10 -1 N ALA A 6 O ASP A 28 SHEET 4 AA2 6 GLY A 209 ASN A 216 -1 O ILE A 210 N LEU A 9 SHEET 5 AA2 6 TRP A 88 THR A 97 -1 N SER A 94 O ALA A 211 SHEET 6 AA2 6 VAL A 179 HIS A 180 -1 O VAL A 179 N VAL A 89 SHEET 1 AA3 6 ALA A 73 ASP A 78 0 SHEET 2 AA3 6 ARG A 60 SER A 66 -1 N VAL A 65 O ALA A 73 SHEET 3 AA3 6 VAL A 47 ASN A 55 -1 N ILE A 53 O SER A 62 SHEET 4 AA3 6 ALA A 186 LYS A 200 -1 O PHE A 195 N ALA A 50 SHEET 5 AA3 6 THR A 103 SER A 117 -1 N LYS A 116 O VAL A 187 SHEET 6 AA3 6 ASN A 124 PHE A 130 -1 O PHE A 128 N PHE A 111 SHEET 1 AA4 7 ALA A 73 ASP A 78 0 SHEET 2 AA4 7 ARG A 60 SER A 66 -1 N VAL A 65 O ALA A 73 SHEET 3 AA4 7 VAL A 47 ASN A 55 -1 N ILE A 53 O SER A 62 SHEET 4 AA4 7 ALA A 186 LYS A 200 -1 O PHE A 195 N ALA A 50 SHEET 5 AA4 7 THR A 103 SER A 117 -1 N LYS A 116 O VAL A 187 SHEET 6 AA4 7 LEU A 154 ARG A 155 -1 O LEU A 154 N ILE A 106 SHEET 7 AA4 7 THR A 147 THR A 148 -1 N THR A 147 O ARG A 155 LINK OE2 GLU A 8 CO CO A 301 1555 1555 2.26 LINK OD2 ASP A 10 CO CO A 301 1555 1555 2.20 LINK OD1 ASP A 10 CA CA A 302 1555 1555 2.38 LINK OD2 ASP A 10 CA CA A 302 1555 1555 2.40 LINK O TYR A 12 CA CA A 302 1555 1555 2.36 LINK OD1 ASN A 14 CA CA A 302 1555 1555 2.47 LINK OD1 ASP A 19 CO CO A 301 1555 1555 2.26 LINK OD2 ASP A 19 CA CA A 302 1555 1555 2.55 LINK NE2 HIS A 24 CO CO A 301 1555 1555 2.38 LINK CO CO A 301 O HOH A 405 1555 1555 2.55 LINK CA CA A 302 O HOH A 407 1555 1555 2.41 CISPEP 1 ALA A 207 ASP A 208 0 -0.21 CRYST1 61.820 86.050 88.600 90.00 90.00 90.00 I 2 2 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 0.016176 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011287 0.00000