HEADER HYDROLASE 16-MAR-20 6YBE TITLE RNASE 3/1 VERSION2 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 3 07-FEB-24 6YBE 1 REMARK REVDAT 2 29-MAR-23 6YBE 1 JRNL REVDAT 1 06-OCT-21 6YBE 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. 1.14 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 43536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.380 REMARK 3 FREE R VALUE TEST SET COUNT : 1906 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 38.4500 - 2.7500 0.95 3122 143 0.1676 0.1728 REMARK 3 2 2.7500 - 2.1800 0.95 3064 139 0.1639 0.1659 REMARK 3 3 2.1800 - 1.9100 0.95 3054 141 0.1492 0.1590 REMARK 3 4 1.9100 - 1.7300 0.95 3067 140 0.1482 0.1577 REMARK 3 5 1.7300 - 1.6100 0.94 2993 137 0.1399 0.1708 REMARK 3 6 1.6100 - 1.5100 0.94 3024 139 0.1352 0.1726 REMARK 3 7 1.5100 - 1.4400 0.93 2954 135 0.1343 0.1574 REMARK 3 8 1.4400 - 1.3700 0.91 2928 135 0.1401 0.1531 REMARK 3 9 1.3700 - 1.3200 0.92 2951 134 0.1285 0.1610 REMARK 3 10 1.3200 - 1.2800 0.92 2922 135 0.1326 0.1674 REMARK 3 11 1.2800 - 1.2400 0.92 2928 133 0.1291 0.1420 REMARK 3 12 1.2400 - 1.2000 0.90 2853 131 0.1307 0.1564 REMARK 3 13 1.2000 - 1.1700 0.90 2897 132 0.1313 0.1800 REMARK 3 14 1.1700 - 1.1400 0.90 2873 132 0.1355 0.1702 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) : 0.076 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.472 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 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 : 0.007 1261 REMARK 3 ANGLE : 1.010 1722 REMARK 3 CHIRALITY : 0.083 167 REMARK 3 PLANARITY : 0.008 239 REMARK 3 DIHEDRAL : 27.231 746 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 6YBE 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_1292107330. 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 : 43663 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 38.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 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 (%): 39.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE PH 5 AND 1 M REMARK 280 SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 14.14909 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.56649 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.14909 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.88500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 24.56649 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 319 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 75.64 -108.59 REMARK 500 GLN A 63 -136.72 -104.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 6YBE A 0 135 PDB 6YBE 6YBE 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 FORMUL 2 HOH *179(H2 O) HELIX 1 AA1 THR A 6 ILE A 16 1 11 HELIX 2 AA2 SER A 21 SER A 25 5 5 HELIX 3 AA3 ARG A 27 MET A 33 1 7 HELIX 4 AA4 MET A 33 ASN A 38 1 6 HELIX 5 AA5 PRO A 53 VAL A 60 1 8 HELIX 6 AA6 CYS A 61 GLN A 63 5 3 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 107 N MET A 82 SHEET 1 AA2 4 GLU A 64 VAL A 66 0 SHEET 2 AA2 4 ASN A 74 ARG A 77 -1 O CYS A 75 N VAL A 66 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 2.02 SSBOND 2 CYS A 43 CYS A 98 1555 1555 2.08 SSBOND 3 CYS A 61 CYS A 113 1555 1555 2.05 SSBOND 4 CYS A 68 CYS A 75 1555 1555 2.05 CISPEP 1 TYR A 95 PRO A 96 0 8.24 CRYST1 43.210 61.770 51.346 90.00 106.88 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 0.023143 0.000000 0.007024 0.00000 SCALE2 0.000000 0.016189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020353 0.00000