HEADER HYDROLASE 08-SEP-19 6SSO TITLE EDN MUTANT L45H 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: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RNASE2, EDN, RNS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EDN, HYDROLASE, PANCREATIC RIBONUCLEASE, EOSINOPHIL-DERIVED KEYWDS 2 NEUROTOXIN EXPDTA X-RAY DIFFRACTION AUTHOR P.FERNANDEZ-MILLAN,G.PRATS-EJARQUE,S.VAZQUEZ-MONTEAGUDO,E.BOIX REVDAT 2 24-JAN-24 6SSO 1 REMARK REVDAT 1 06-OCT-21 6SSO 0 JRNL AUTH P.FERNANDEZ-MILLAN,G.PRATS-EJARQUE,S.VAZQUEZ-MONTEAGUDO, JRNL AUTH 2 E.BOIX JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF NEW FAMILY JRNL TITL 2 ENZYMES DERIVATES FROM HUMAN RNASE 1 AND 3 WITH JRNL TITL 3 ANTIMICROBIAL AND RIBONUCLEASE ACTIVITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.21 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) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38675 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 : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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 38.4890 - 2.9180 0.99 2781 150 0.1549 0.1592 REMARK 3 2 2.9180 - 2.3162 0.99 2683 143 0.1499 0.1444 REMARK 3 3 2.3162 - 2.0235 1.00 2649 146 0.1363 0.1411 REMARK 3 4 2.0235 - 1.8385 0.99 2622 144 0.1283 0.1385 REMARK 3 5 1.8385 - 1.7067 1.00 2645 143 0.1286 0.1351 REMARK 3 6 1.7067 - 1.6061 1.00 2590 154 0.1198 0.1488 REMARK 3 7 1.6061 - 1.5256 0.99 2593 135 0.1177 0.1614 REMARK 3 8 1.5256 - 1.4592 0.99 2581 141 0.1161 0.1680 REMARK 3 9 1.4592 - 1.4030 1.00 2604 142 0.1188 0.1495 REMARK 3 10 1.4030 - 1.3546 1.00 2584 138 0.1172 0.1544 REMARK 3 11 1.3546 - 1.3123 0.99 2577 135 0.1195 0.1846 REMARK 3 12 1.3123 - 1.2747 1.00 2600 151 0.1207 0.1513 REMARK 3 13 1.2747 - 1.2412 1.00 2574 133 0.1210 0.1624 REMARK 3 14 1.2412 - 1.2110 0.99 2596 141 0.1213 0.1555 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.40 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6SSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104239. 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 : 7.0 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) : 0.979256 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 : 38717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 38.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 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: 1GQV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE, PH 7 AND 1.6 REMARK 280 M SODIUM ACETATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 297K 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 21.06000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.31500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.23500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.31500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.23500 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: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 ASN A 17 61.35 -102.77 REMARK 500 SER A 89 68.85 -161.31 REMARK 500 ASN A 92 84.19 -152.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 132 0.15 SIDE CHAIN 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 ACT A 201 DBREF 6SSO A 0 134 UNP P10153 RNAS2_HUMAN 27 161 SEQADV 6SSO MET A 0 UNP P10153 VAL 27 CONFLICT SEQADV 6SSO HIS A 45 UNP P10153 LEU 72 ENGINEERED MUTATION 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 HIS 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 ACT A 201 7 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *160(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 GLY A 56 1 10 HELIX 4 AA4 ASN A 92 CYS A 96 5 5 SHEET 1 AA1 4 GLN A 40 LEU A 44 0 SHEET 2 AA1 4 VAL A 78 THR A 87 -1 O CYS A 83 N ASN A 41 SHEET 3 AA1 4 ARG A 97 ASN A 113 -1 O ARG A 97 N THR A 86 SHEET 4 AA1 4 CYS A 71 HIS A 73 -1 N HIS A 72 O VAL A 109 SHEET 1 AA2 4 GLN A 40 LEU A 44 0 SHEET 2 AA2 4 VAL A 78 THR A 87 -1 O CYS A 83 N ASN A 41 SHEET 3 AA2 4 ARG A 97 ASN A 113 -1 O ARG A 97 N THR A 86 SHEET 4 AA2 4 VAL A 125 ILE A 134 -1 O VAL A 128 N ALA A 110 SSBOND 1 CYS A 23 CYS A 83 1555 1555 2.03 SSBOND 2 CYS A 37 CYS A 96 1555 1555 2.02 SSBOND 3 CYS A 55 CYS A 111 1555 1555 2.04 SSBOND 4 CYS A 62 CYS A 71 1555 1555 2.05 SITE 1 AC1 7 THR A 46 ASN A 50 SER A 76 VAL A 78 SITE 2 AC1 7 TYR A 107 HOH A 306 HOH A 330 CRYST1 42.120 52.470 56.630 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 0.023742 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017658 0.00000