HEADER PROTEIN BINDING 09-SEP-24 9GQM TITLE STRUCTURAL CHARACTERIZATION OF GLUCOSE- AND FUCOSE-BINDING SITES IN TITLE 2 HUMAN RNASE2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SECRETORY RIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EOSINOPHIL-DERIVED NEUROTOXIN,RNASE UPI-2,RIBONUCLEASE 2, COMPND 5 RNASE 2,RIBONUCLEASE US; COMPND 6 EC: 4.6.1.18; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 3 ORGANISM_TAXID: 866768; SOURCE 4 GENE: RNASE2, EDN, RNS2; SOURCE 5 EXPRESSION_SYSTEM: EXPRESSION VECTOR PET-MOD; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1685505 KEYWDS MONOSACCHARIDE, GLUCOSE, FUCOSE, IMMUNE SYSTEM, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.XINCHENG,L.JIARUI,G.PRATS-EJARQUE,E.BOIX REVDAT 1 18-MAR-26 9GQM 0 JRNL AUTH K.XINCHENG,L.JIARUI,G.PRATS-EJARQUE,E.BOIX JRNL TITL STRUCTURAL CHARACTERIZATION OF GLUCOSE- AND FUCOSE-BINDING JRNL TITL 2 SITES IN HUMAN RNASE2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 3 NUMBER OF REFLECTIONS : 56643 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.550 REMARK 3 FREE R VALUE TEST SET COUNT : 2008 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 38.6000 - 2.4400 1.00 4782 180 0.1447 0.1587 REMARK 3 2 2.4400 - 1.9400 1.00 4603 169 0.1480 0.1719 REMARK 3 3 1.9400 - 1.7000 1.00 4551 168 0.1431 0.1682 REMARK 3 4 1.7000 - 1.5400 1.00 4540 155 0.1325 0.1323 REMARK 3 5 1.5400 - 1.4300 1.00 4496 171 0.1262 0.1460 REMARK 3 6 1.4300 - 1.3500 1.00 4505 167 0.1233 0.1412 REMARK 3 7 1.3500 - 1.2800 1.00 4494 161 0.1188 0.1371 REMARK 3 8 1.2800 - 1.2200 1.00 4465 173 0.1166 0.1404 REMARK 3 9 1.2200 - 1.1800 1.00 4483 158 0.1113 0.1234 REMARK 3 10 1.1800 - 1.1300 0.97 4361 156 0.1107 0.1106 REMARK 3 11 1.1300 - 1.1000 0.87 3863 143 0.1170 0.1340 REMARK 3 12 1.1000 - 1.0700 0.67 3021 107 0.1257 0.1761 REMARK 3 13 1.0700 - 1.0400 0.41 1832 79 0.1514 0.1462 REMARK 3 14 1.0400 - 1.0100 0.14 639 21 0.1920 0.2702 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.062 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.489 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.55 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 1235 REMARK 3 ANGLE : 0.939 1696 REMARK 3 CHIRALITY : 0.083 187 REMARK 3 PLANARITY : 0.008 229 REMARK 3 DIHEDRAL : 7.103 178 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 9GQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292141580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-24 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56650 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.010 REMARK 200 RESOLUTION RANGE LOW (A) : 38.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 30.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE TRIHYDRATE, PH REMARK 280 7.0, 12% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.15K 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 20.94250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.26700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.41450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.26700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.94250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.41450 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 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 SER A 89 69.91 -153.42 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 528 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A 529 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 530 DISTANCE = 7.10 ANGSTROMS REMARK 525 HOH A 531 DISTANCE = 7.97 ANGSTROMS 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 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 53 OD1 REMARK 620 2 HOH A 375 O 142.7 REMARK 620 3 HOH A 395 O 117.1 72.8 REMARK 620 4 HOH A 419 O 86.3 111.9 135.7 REMARK 620 N 1 2 3 DBREF 9GQM A 1 134 UNP P10153 RNAS2_HUMAN 28 161 SEQADV 9GQM MET A 0 UNP P10153 INITIATING METHIONINE SEQRES 1 A 135 MET LYS PRO PRO GLN PHE THR TRP ALA GLN TRP PHE GLU SEQRES 2 A 135 THR GLN HIS ILE ASN MET THR SER GLN GLN CYS THR ASN SEQRES 3 A 135 ALA MET GLN VAL ILE ASN ASN TYR GLN ARG ARG CYS LYS SEQRES 4 A 135 ASN GLN ASN THR PHE LEU LEU THR THR PHE ALA ASN VAL SEQRES 5 A 135 VAL ASN VAL CYS GLY ASN PRO ASN MET THR CYS PRO SER SEQRES 6 A 135 ASN LYS THR ARG LYS ASN CYS HIS HIS SER GLY SER GLN SEQRES 7 A 135 VAL PRO LEU ILE HIS CYS ASN LEU THR THR PRO SER PRO SEQRES 8 A 135 GLN ASN ILE SER ASN CYS ARG TYR ALA GLN THR PRO ALA SEQRES 9 A 135 ASN MET PHE TYR ILE VAL ALA CYS ASP ASN ARG ASP GLN SEQRES 10 A 135 ARG ARG ASP PRO PRO GLN TYR PRO VAL VAL PRO VAL HIS SEQRES 11 A 135 LEU ASP ARG ILE ILE HET PEG A 201 7 HET FUC A 202 11 HET ACT A 203 4 HET GLC A 204 12 HET NA A 205 1 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM ACT ACETATE ION HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 PEG C4 H10 O3 FORMUL 3 FUC C6 H12 O5 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 GLC C6 H12 O6 FORMUL 6 NA NA 1+ FORMUL 7 HOH *231(H2 O) HELIX 1 AA1 THR A 6 ILE A 16 1 11 HELIX 2 AA2 GLN A 22 ARG A 35 1 14 HELIX 3 AA3 THR A 47 CYS A 55 1 9 HELIX 4 AA4 ASN A 92 CYS A 96 5 5 SHEET 1 AA1 3 GLN A 40 LEU A 44 0 SHEET 2 AA1 3 VAL A 78 THR A 87 -1 O ILE A 81 N PHE A 43 SHEET 3 AA1 3 ARG A 97 MET A 105 -1 O ALA A 99 N ASN A 84 SHEET 1 AA2 4 ASN A 59 MET A 60 0 SHEET 2 AA2 4 CYS A 71 HIS A 73 -1 O CYS A 71 N MET A 60 SHEET 3 AA2 4 TYR A 107 ASN A 113 -1 O VAL A 109 N HIS A 72 SHEET 4 AA2 4 VAL A 125 ILE A 133 -1 O VAL A 128 N ALA A 110 SSBOND 1 CYS A 23 CYS A 83 1555 1555 2.04 SSBOND 2 CYS A 37 CYS A 96 1555 1555 2.02 SSBOND 3 CYS A 55 CYS A 111 1555 1555 2.05 SSBOND 4 CYS A 62 CYS A 71 1555 1555 2.05 LINK OD1 ASN A 53 NA NA A 205 1555 1555 2.71 LINK NA NA A 205 O HOH A 375 1555 3544 2.76 LINK NA NA A 205 O HOH A 395 1555 3544 2.76 LINK NA NA A 205 O HOH A 419 1555 1555 2.75 CRYST1 41.885 52.829 56.534 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 0.023875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017688 0.00000 CONECT 227 734 CONECT 361 829 CONECT 488 1200 CONECT 502 958 CONECT 558 635 CONECT 635 558 CONECT 734 227 CONECT 829 361 CONECT 958 502 CONECT 1166 1167 1168 CONECT 1167 1166 CONECT 1168 1166 1169 CONECT 1169 1168 1170 CONECT 1170 1169 1171 CONECT 1171 1170 1172 CONECT 1172 1171 CONECT 1173 1174 1179 1183 CONECT 1174 1173 1175 1180 CONECT 1175 1174 1176 1181 CONECT 1176 1175 1177 1182 CONECT 1177 1176 1178 1183 CONECT 1178 1177 CONECT 1179 1173 CONECT 1180 1174 CONECT 1181 1175 CONECT 1182 1176 CONECT 1183 1173 1177 CONECT 1184 1185 1186 1187 CONECT 1185 1184 CONECT 1186 1184 CONECT 1187 1184 CONECT 1188 1189 1194 1198 CONECT 1189 1188 1190 1195 CONECT 1190 1189 1191 1196 CONECT 1191 1190 1192 1197 CONECT 1192 1191 1193 1198 CONECT 1193 1192 1199 CONECT 1194 1188 CONECT 1195 1189 CONECT 1196 1190 CONECT 1197 1191 CONECT 1198 1188 1192 CONECT 1199 1193 CONECT 1200 488 1319 CONECT 1319 1200 MASTER 248 0 5 4 7 0 0 6 1355 1 45 11 END