HEADER PROTEIN BINDING 04-SEP-24 9GNT TITLE STRUCTURAL CHARACTERIZATION OF A GLUCOSE-BINDING SITE IN 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, RNASE, IMMUNE SYSTEM, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.XINCHENG,L.JIARUI,G.PRATS-EJARQUE,E.BOIX REVDAT 1 18-MAR-26 9GNT 0 JRNL AUTH K.XINCHENG,L.JIARUI,G.PRATS-EJARQUE,E.BOIX JRNL TITL STRUCTURAL CHARACTERIZATION OF A GLUCOSE-BINDING SITE IN JRNL TITL 2 HUMAN RNASE2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.31 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) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.2 REMARK 3 NUMBER OF REFLECTIONS : 25886 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1297 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 33.7100 - 2.7200 0.99 3422 181 0.1486 0.1916 REMARK 3 2 2.7200 - 2.1600 0.99 3285 177 0.1473 0.1846 REMARK 3 3 2.1600 - 1.8900 1.00 3272 173 0.1403 0.1910 REMARK 3 4 1.8900 - 1.7200 0.99 3244 175 0.1550 0.2074 REMARK 3 5 1.7200 - 1.5900 1.00 3254 167 0.1877 0.2295 REMARK 3 6 1.5900 - 1.5000 0.99 3195 168 0.1989 0.2807 REMARK 3 7 1.5000 - 1.4200 0.82 2681 144 0.2437 0.3366 REMARK 3 8 1.4200 - 1.3600 0.49 1597 76 0.2658 0.3002 REMARK 3 9 1.3600 - 1.3100 0.20 639 36 0.2862 0.3637 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) : 0.134 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.993 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.68 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 1207 REMARK 3 ANGLE : 0.980 1655 REMARK 3 CHIRALITY : 0.085 175 REMARK 3 PLANARITY : 0.006 225 REMARK 3 DIHEDRAL : 27.754 170 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 9GNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292141502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-23 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 : 25888 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 33.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 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 (%): 39.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M CITRIC ACID, 0.05M BIS-TRIS REMARK 280 PROPANE PH 5.0, 16%W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, REMARK 280 SITTING 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 20.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.38500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.51200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.38500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.51200 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 74.50 -164.91 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 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 24 OG1 REMARK 620 2 TYR A 98 O 71.9 REMARK 620 3 GLN A 100 OE1 167.5 117.2 REMARK 620 4 HOH A 328 O 80.0 121.3 100.6 REMARK 620 N 1 2 3 DBREF 9GNT A 1 134 UNP P10153 RNAS2_HUMAN 28 161 SEQADV 9GNT 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 CIT A 201 13 HET CIT A 202 13 HET CIT A 203 13 HET GLC A 204 12 HET NA A 205 1 HET CL A 206 1 HETNAM CIT CITRIC ACID HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 CIT 3(C6 H8 O7) FORMUL 5 GLC C6 H12 O6 FORMUL 6 NA NA 1+ FORMUL 7 CL CL 1- FORMUL 8 HOH *200(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 CYS A 83 N ASN A 41 SHEET 3 AA1 3 ARG A 97 MET A 105 -1 O ALA A 99 N ASN A 84 SHEET 1 AA2 3 CYS A 71 HIS A 73 0 SHEET 2 AA2 3 TYR A 107 ASN A 113 -1 O VAL A 109 N HIS A 72 SHEET 3 AA2 3 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 2.05 SSBOND 2 CYS A 37 CYS A 96 1555 1555 2.03 SSBOND 3 CYS A 55 CYS A 111 1555 1555 2.03 SSBOND 4 CYS A 62 CYS A 71 1555 1555 2.04 LINK OG1 THR A 24 NA NA A 205 1555 1555 3.13 LINK O TYR A 98 NA NA A 205 1555 1555 2.84 LINK OE1 GLN A 100 NA NA A 205 1555 1555 2.74 LINK NA NA A 205 O HOH A 328 1555 1555 2.83 CRYST1 41.900 53.024 56.770 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 0.023866 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018859 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017615 0.00000 CONECT 218 703 CONECT 224 1178 CONECT 344 798 CONECT 485 927 CONECT 541 612 CONECT 612 541 CONECT 703 218 CONECT 798 344 CONECT 813 1178 CONECT 834 1178 CONECT 927 485 CONECT 1127 1128 1129 1130 CONECT 1128 1127 CONECT 1129 1127 CONECT 1130 1127 1131 CONECT 1131 1130 1132 1133 1137 CONECT 1132 1131 CONECT 1133 1131 1134 CONECT 1134 1133 1135 1136 CONECT 1135 1134 CONECT 1136 1134 CONECT 1137 1131 1138 1139 CONECT 1138 1137 CONECT 1139 1137 CONECT 1140 1141 1142 1143 CONECT 1141 1140 CONECT 1142 1140 CONECT 1143 1140 1144 CONECT 1144 1143 1145 1146 1150 CONECT 1145 1144 CONECT 1146 1144 1147 CONECT 1147 1146 1148 1149 CONECT 1148 1147 CONECT 1149 1147 CONECT 1150 1144 1151 1152 CONECT 1151 1150 CONECT 1152 1150 CONECT 1153 1154 1155 1156 CONECT 1154 1153 CONECT 1155 1153 CONECT 1156 1153 1157 CONECT 1157 1156 1158 1159 1163 CONECT 1158 1157 CONECT 1159 1157 1160 CONECT 1160 1159 1161 1162 CONECT 1161 1160 CONECT 1162 1160 CONECT 1163 1157 1164 1165 CONECT 1164 1163 CONECT 1165 1163 CONECT 1166 1167 1172 1176 CONECT 1167 1166 1168 1173 CONECT 1168 1167 1169 1174 CONECT 1169 1168 1170 1175 CONECT 1170 1169 1171 1176 CONECT 1171 1170 1177 CONECT 1172 1166 CONECT 1173 1167 CONECT 1174 1168 CONECT 1175 1169 CONECT 1176 1166 1170 CONECT 1177 1171 CONECT 1178 224 813 834 1207 CONECT 1207 1178 MASTER 227 0 6 4 6 0 0 6 1342 1 64 11 END