HEADER PROTEIN BINDING 04-SEP-24 9GO4 TITLE STRUCTURAL CHARACTERIZATION OF CITRATE-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 TRICARBOXYLATE, CITRATE, RNASE, IMMUNE SYSTEM, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.XINCHENG,L.JIARUI,G.PRATS-EJARQUE,E.BOIX REVDAT 1 18-MAR-26 9GO4 0 JRNL AUTH K.XINCHENG,L.JIARUI,G.PRATS-EJARQUE,E.BOIX JRNL TITL STRUCTURAL CHARACTERIZATION OF CITRATE-BINDING SITE IN HUMAN JRNL TITL 2 RNASE2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.17 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.6 REMARK 3 NUMBER OF REFLECTIONS : 32955 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1676 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 33.5300 - 2.6900 1.00 3515 183 0.1497 0.1780 REMARK 3 2 2.6900 - 2.1300 0.97 3278 180 0.1487 0.1772 REMARK 3 3 2.1300 - 1.8600 1.00 3336 170 0.1407 0.1861 REMARK 3 4 1.8600 - 1.6900 1.00 3317 190 0.1464 0.1852 REMARK 3 5 1.6900 - 1.5700 1.00 3304 160 0.1402 0.1902 REMARK 3 6 1.5700 - 1.4800 1.00 3271 192 0.1382 0.1787 REMARK 3 7 1.4800 - 1.4100 0.98 3229 158 0.1483 0.2237 REMARK 3 8 1.4100 - 1.3400 0.86 2790 163 0.1678 0.2100 REMARK 3 9 1.3400 - 1.2900 0.68 2242 122 0.2127 0.2036 REMARK 3 10 1.2900 - 1.2500 0.52 1669 96 0.2254 0.2452 REMARK 3 11 1.2500 - 1.2100 0.31 1036 48 0.2481 0.3154 REMARK 3 12 1.2100 - 1.1700 0.09 292 14 0.2545 0.3205 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) : 0.098 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.76 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 1242 REMARK 3 ANGLE : 0.939 1699 REMARK 3 CHIRALITY : 0.083 175 REMARK 3 PLANARITY : 0.009 235 REMARK 3 DIHEDRAL : 23.444 180 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 9GO4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292141529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-22 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 : 32960 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 38.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 42.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.30 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 (%): 39.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE DIBASIC, 20% REMARK 280 W/V POLYETHYLENE GLYCOL 3,350, PH 5.1, 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 20.83900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.22650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.20900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.22650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.83900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.20900 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: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 64.65 -171.55 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 209 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 13 O REMARK 620 2 ASN A 17 O 97.1 REMARK 620 3 HOH A 340 O 87.2 66.0 REMARK 620 4 HOH A 352 O 80.9 66.5 6.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 17 OD1 REMARK 620 2 HOH A 349 O 122.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 210 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 345 O REMARK 620 2 HOH A 368 O 74.6 REMARK 620 3 HOH A 404 O 111.2 129.1 REMARK 620 N 1 2 DBREF 9GO4 A 1 134 UNP P10153 RNAS2_HUMAN 28 161 SEQADV 9GO4 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 FMT A 203 3 HET PEG A 204 7 HET CIT A 205 13 HET ACT A 206 4 HET FMT A 207 3 HET NA A 208 1 HET NA A 209 1 HET NA A 210 1 HETNAM CIT CITRIC ACID HETNAM FMT FORMIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ACT ACETATE ION HETNAM NA SODIUM ION FORMUL 2 CIT 3(C6 H8 O7) FORMUL 4 FMT 2(C H2 O2) FORMUL 5 PEG C4 H10 O3 FORMUL 7 ACT C2 H3 O2 1- FORMUL 9 NA 3(NA 1+) FORMUL 12 HOH *210(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 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 2.06 SSBOND 2 CYS A 37 CYS A 96 1555 1555 2.03 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 O THR A 13 NA NA A 209 1555 4555 2.75 LINK OD1 ASN A 17 NA NA A 208 1555 1555 2.72 LINK O ASN A 17 NA NA A 209 1555 4555 2.63 LINK NA NA A 208 O HOH A 349 1555 2455 2.92 LINK NA NA A 209 O HOH A 340 1555 1555 2.74 LINK NA NA A 209 O HOH A 352 1555 4455 2.87 LINK NA NA A 210 O HOH A 345 1555 1555 2.83 LINK NA NA A 210 O HOH A 368 1555 1555 2.82 LINK NA NA A 210 O HOH A 404 1555 3554 2.78 CRYST1 41.678 52.418 56.453 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 0.023993 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017714 0.00000 CONECT 172 1214 CONECT 227 726 CONECT 353 821 CONECT 494 958 CONECT 550 627 CONECT 627 550 CONECT 726 227 CONECT 821 353 CONECT 958 494 CONECT 1158 1159 1160 1161 CONECT 1159 1158 CONECT 1160 1158 CONECT 1161 1158 1162 CONECT 1162 1161 1163 1164 1168 CONECT 1163 1162 CONECT 1164 1162 1165 CONECT 1165 1164 1166 1167 CONECT 1166 1165 CONECT 1167 1165 CONECT 1168 1162 1169 1170 CONECT 1169 1168 CONECT 1170 1168 CONECT 1171 1172 1173 1174 CONECT 1172 1171 CONECT 1173 1171 CONECT 1174 1171 1175 CONECT 1175 1174 1176 1177 1181 CONECT 1176 1175 CONECT 1177 1175 1178 CONECT 1178 1177 1179 1180 CONECT 1179 1178 CONECT 1180 1178 CONECT 1181 1175 1182 1183 CONECT 1182 1181 CONECT 1183 1181 CONECT 1184 1185 1186 CONECT 1185 1184 CONECT 1186 1184 CONECT 1187 1188 1189 CONECT 1188 1187 CONECT 1189 1187 1190 CONECT 1190 1189 1191 CONECT 1191 1190 1192 CONECT 1192 1191 1193 CONECT 1193 1192 CONECT 1194 1195 1196 1197 CONECT 1195 1194 CONECT 1196 1194 CONECT 1197 1194 1198 CONECT 1198 1197 1199 1200 1204 CONECT 1199 1198 CONECT 1200 1198 1201 CONECT 1201 1200 1202 1203 CONECT 1202 1201 CONECT 1203 1201 CONECT 1204 1198 1205 1206 CONECT 1205 1204 CONECT 1206 1204 CONECT 1207 1208 1209 1210 CONECT 1208 1207 CONECT 1209 1207 CONECT 1210 1207 CONECT 1211 1212 1213 CONECT 1212 1211 CONECT 1213 1211 CONECT 1214 172 CONECT 1215 1256 CONECT 1216 1261 1284 CONECT 1256 1215 CONECT 1261 1216 CONECT 1284 1216 MASTER 250 0 10 4 7 0 0 6 1358 1 71 11 END