HEADER HYDROLASE 16-MAR-20 6YBC TITLE RNASE 3/1 VERSION2 PHOSPHATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE 3/1 VERSION2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASE 3/1 VERSION2, HYDROLASE, PANCREATIC RIBONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR P.FERNANDEZ-MILLAN,G.PRATS-EJARQUE,S.VAZQUEZ-MONTEAGUDO,E.BOIX REVDAT 4 23-OCT-24 6YBC 1 REMARK REVDAT 3 07-FEB-24 6YBC 1 REMARK REVDAT 2 29-MAR-23 6YBC 1 JRNL REVDAT 1 06-OCT-21 6YBC 0 JRNL AUTH P.FERNANDEZ-MILLAN,S.VAZQUEZ-MONTEAGUDO,E.BOIX, JRNL AUTH 2 G.PRATS-EJARQUE JRNL TITL EXPLORING THE RNASE A SCAFFOLD TO COMBINE CATALYTIC AND JRNL TITL 2 ANTIMICROBIAL ACTIVITIES. STRUCTURAL CHARACTERIZATION OF JRNL TITL 3 RNASE 3/1 CHIMERAS. JRNL REF FRONT MOL BIOSCI V. 9 64717 2022 JRNL REFN ESSN 2296-889X JRNL PMID 36188223 JRNL DOI 10.3389/FMOLB.2022.964717 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 21291 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.390 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 38.5800 - 3.5800 0.99 1414 147 0.1673 0.2185 REMARK 3 2 3.5800 - 2.8400 1.00 1396 144 0.1537 0.1792 REMARK 3 3 2.8400 - 2.4800 1.00 1381 144 0.1460 0.1684 REMARK 3 4 2.4800 - 2.2500 1.00 1389 143 0.1390 0.2024 REMARK 3 5 2.2500 - 2.0900 0.99 1382 142 0.1316 0.1735 REMARK 3 6 2.0900 - 1.9700 0.99 1364 142 0.1339 0.1638 REMARK 3 7 1.9700 - 1.8700 0.99 1366 141 0.1346 0.2007 REMARK 3 8 1.8700 - 1.7900 0.99 1363 142 0.1315 0.1911 REMARK 3 9 1.7900 - 1.7200 0.99 1380 143 0.1341 0.2018 REMARK 3 10 1.7200 - 1.6600 0.99 1363 141 0.1334 0.2047 REMARK 3 11 1.6600 - 1.6100 0.99 1371 143 0.1389 0.1986 REMARK 3 12 1.6100 - 1.5600 0.99 1384 143 0.1409 0.1718 REMARK 3 13 1.5600 - 1.5200 0.99 1353 141 0.1430 0.2252 REMARK 3 14 1.5200 - 1.4900 1.00 1386 143 0.1620 0.2331 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.142 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.348 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.78 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 1277 REMARK 3 ANGLE : 0.972 1745 REMARK 3 CHIRALITY : 0.078 166 REMARK 3 PLANARITY : 0.008 233 REMARK 3 DIHEDRAL : 25.625 745 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 6YBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-19 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) : 0.9792568 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21301 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 38.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 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 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: 2K11 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE, PH 6.5 AND 1 M REMARK 280 AMMONIUM PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 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+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -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 14.28044 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.70465 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.28044 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.87000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 24.70465 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 446 LIES ON A SPECIAL POSITION. 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 134 REMARK 465 VAL A 135 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 HIS A 51 79.91 -101.76 REMARK 500 HIS A 51 79.91 -104.37 REMARK 500 GLN A 63 -137.49 -103.15 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 PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 206 DBREF 6YBC A 0 135 PDB 6YBC 6YBC 0 135 SEQRES 1 A 136 MET ARG PRO PRO GLN PHE THR ARG ALA GLN TRP PHE ALA SEQRES 2 A 136 ILE GLN HIS ILE ASP SER ASP SER SER PRO SER SER SER SEQRES 3 A 136 SER ARG TYR CYS THR ILE ALA MET ARG ALA ILE ASN ASN SEQRES 4 A 136 TYR ARG TRP ARG CYS LYS PRO VAL ASN THR PHE VAL HIS SEQRES 5 A 136 GLU PRO LEU VAL ASP VAL GLN ASN VAL CYS PHE GLN GLU SEQRES 6 A 136 LYS VAL THR CYS LYS ASN GLY GLN GLY ASN CYS TYR ARG SEQRES 7 A 136 SER ARG PHE ARG MET HIS ILE THR ASP CYS ARG LEU THR SEQRES 8 A 136 ASN GLY SER ARG TYR PRO ASN CYS ARG TYR ARG THR ARG SEQRES 9 A 136 PRO GLY ARG ARG HIS ILE ILE VAL ALA CYS GLU ASN ARG SEQRES 10 A 136 ASP PRO ARG ASP SER PRO ARG TYR PRO TYR VAL PRO VAL SEQRES 11 A 136 HIS PHE ASP ALA SER VAL HET GOL A 201 14 HET PO4 A 202 5 HET PO4 A 203 10 HET PO4 A 204 15 HET PO4 A 205 5 HET PO4 A 206 5 HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 PO4 5(O4 P 3-) FORMUL 8 HOH *147(H2 O) HELIX 1 AA1 THR A 6 ILE A 16 1 11 HELIX 2 AA2 ARG A 27 ASN A 38 1 12 HELIX 3 AA3 PRO A 53 ASN A 59 1 7 HELIX 4 AA4 VAL A 60 GLN A 63 5 4 SHEET 1 AA1 3 VAL A 46 VAL A 50 0 SHEET 2 AA1 3 MET A 82 LEU A 89 -1 O CYS A 87 N ASN A 47 SHEET 3 AA1 3 TYR A 100 ARG A 107 -1 O ARG A 101 N ARG A 88 SHEET 1 AA2 4 GLU A 64 VAL A 66 0 SHEET 2 AA2 4 ASN A 74 ARG A 77 -1 O ARG A 77 N GLU A 64 SHEET 3 AA2 4 ILE A 110 ASN A 115 -1 O CYS A 113 N ASN A 74 SHEET 4 AA2 4 TYR A 126 PHE A 131 -1 O VAL A 129 N ALA A 112 SSBOND 1 CYS A 29 CYS A 87 1555 1555 2.04 SSBOND 2 CYS A 43 CYS A 98 1555 1555 2.07 SSBOND 3 CYS A 61 CYS A 113 1555 1555 2.00 SSBOND 4 CYS A 68 CYS A 75 1555 1555 2.05 CISPEP 1 TYR A 95 PRO A 96 0 9.49 SITE 1 AC1 6 ASN A 38 ARG A 40 TRP A 41 PRO A 104 SITE 2 AC1 6 GLY A 105 HOH A 334 SITE 1 AC2 10 CYS A 61 PHE A 62 TYR A 76 THR A 90 SITE 2 AC2 10 GLY A 92 ARG A 99 TYR A 126 PO4 A 205 SITE 3 AC2 10 HOH A 303 HOH A 373 SITE 1 AC3 8 GLN A 4 TYR A 39 PHE A 80 ARG A 81 SITE 2 AC3 8 PRO A 96 ARG A 106 ARG A 116 HOH A 385 SITE 1 AC4 10 PHE A 11 GLN A 14 HIS A 15 LYS A 44 SITE 2 AC4 10 VAL A 129 HIS A 130 HOH A 306 HOH A 338 SITE 3 AC4 10 HOH A 346 HOH A 376 SITE 1 AC5 9 LYS A 65 THR A 90 ASN A 91 GLY A 92 SITE 2 AC5 9 ARG A 101 PO4 A 202 HOH A 303 HOH A 309 SITE 3 AC5 9 HOH A 371 SITE 1 AC6 3 ARG A 81 ARG A 107 HIS A 108 CRYST1 43.160 61.740 51.521 90.00 106.46 90.00 I 1 2 1 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 0.023170 0.000000 0.006846 0.00000 SCALE2 0.000000 0.016197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020239 0.00000