HEADER DNA BINDING PROTEIN 17-NOV-21 7W05 TITLE 12 MUTANT RIBONUCLEASE FROM HERICIUM ERINACEUS GMP BINDING FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE T1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HERICIUM ERINACEUS; SOURCE 3 ORGANISM_COMMON: LION'S MANE MUSHROOM, HYDNUM ERINACEUS; SOURCE 4 ORGANISM_TAXID: 91752; SOURCE 5 GENE: RNHE1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CATALYTIC ACTIVITY ENZYME ANTI TUMOR ACTIVITY NUCLEIC ACID BINDING KEYWDS 2 RNA BINDING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.TAKEBE,T.CHIDA,M.SUZUKI,T.ITAGAKI,Y.MORITA,N.UZAWA,H.KOBAYASHI REVDAT 2 29-NOV-23 7W05 1 REMARK REVDAT 1 23-NOV-22 7W05 0 JRNL AUTH K.TAKEBE,T.CHIDA,M.SUZUKI,N.UZAWA,H.KOBAYASHI JRNL TITL 12 MUTANT RIBONUCLEASE FROM HERICIUM ERINACEUS GMP BINDING JRNL TITL 2 FORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 21999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1089 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 11.9947 - 2.5726 1.00 2794 148 0.1393 0.1658 REMARK 3 2 2.5726 - 2.0453 1.00 2668 140 0.1289 0.1719 REMARK 3 3 2.0453 - 1.7877 1.00 2640 134 0.1254 0.1489 REMARK 3 4 1.7877 - 1.6247 1.00 2641 130 0.1330 0.1588 REMARK 3 5 1.6247 - 1.5085 1.00 2591 142 0.1336 0.1612 REMARK 3 6 1.5085 - 1.4197 1.00 2636 134 0.1380 0.1645 REMARK 3 7 1.4197 - 1.3487 1.00 2591 127 0.1575 0.1717 REMARK 3 8 1.3487 - 1.2900 0.92 2349 134 0.1774 0.2245 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.46 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 7W05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1300025498. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-21 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22027 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 REMARK 200 RESOLUTION RANGE LOW (A) : 46.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 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: MOLREP REMARK 200 STARTING MODEL: 6LS1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CADMIUM CHLORIDE HYDRATE, 0.1 M REMARK 280 SODIUM ACETATE TRIHYDRATE PH 4.6, 30% V/V POLYETHYLENE GLYCOL REMARK 280 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 17.29450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.76200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.76200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.29450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.15500 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: 470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 5 CB CYS A 5 SG -0.240 REMARK 500 CYS A 5 CB CYS A 5 SG -0.302 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 5 CA - CB - SG ANGL. DEV. = 21.2 DEGREES REMARK 500 CYS A 5 CA - CB - SG ANGL. DEV. = 16.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7W05 A 1 100 UNP B1Q4V2 B1Q4V2_HERER 25 124 SEQADV 7W05 ASN A 19 UNP B1Q4V2 ASP 43 ENGINEERED MUTATION SEQADV 7W05 ASN A 22 UNP B1Q4V2 ASP 46 ENGINEERED MUTATION SEQADV 7W05 GLN A 25 UNP B1Q4V2 GLU 49 ENGINEERED MUTATION SEQADV 7W05 ASN A 31 UNP B1Q4V2 ASP 55 ENGINEERED MUTATION SEQADV 7W05 ASN A 38 UNP B1Q4V2 ASP 62 ENGINEERED MUTATION SEQADV 7W05 GLN A 50 UNP B1Q4V2 GLU 74 ENGINEERED MUTATION SEQADV 7W05 GLN A 57 UNP B1Q4V2 GLU 81 ENGINEERED MUTATION SEQADV 7W05 GLN A 76 UNP B1Q4V2 GLU 100 ENGINEERED MUTATION SEQADV 7W05 ASN A 77 UNP B1Q4V2 ASP 101 ENGINEERED MUTATION SEQADV 7W05 ASN A 79 UNP B1Q4V2 ASP 103 ENGINEERED MUTATION SEQADV 7W05 GLN A 92 UNP B1Q4V2 GLU 116 ENGINEERED MUTATION SEQADV 7W05 ASN A 93 UNP B1Q4V2 ASP 117 ENGINEERED MUTATION SEQRES 1 A 100 GLN SER GLY GLY CYS SER CYS ALA GLY ARG SER TYR SER SEQRES 2 A 100 SER SER ASN ILE ALA ASN ALA ILE ASN GLN ALA GLN GLY SEQRES 3 A 100 ARG GLY GLY GLY ASN TYR PRO HIS GLN TYR HIS ASN TYR SEQRES 4 A 100 GLU GLY PHE SER PHE PRO SER CYS ARG GLY GLN PHE PHE SEQRES 5 A 100 GLU TYR PRO LEU GLN ARG SER GLY VAL TYR THR GLY GLY SEQRES 6 A 100 SER PRO GLY ALA ASP ARG VAL ILE TYR ASP GLN ASN GLY SEQRES 7 A 100 ASN PHE CYS ALA CYS LEU THR HIS THR GLY ALA SER THR SEQRES 8 A 100 GLN ASN GLY PHE VAL GLU CYS ASN PHE HET GMP A 201 20 HET PEG A 202 7 HETNAM GMP GUANOSINE HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 GMP C10 H13 N5 O5 FORMUL 3 PEG C4 H10 O3 FORMUL 4 HOH *130(H2 O) HELIX 1 AA1 SER A 13 GLY A 26 1 14 SHEET 1 AA1 2 CYS A 5 CYS A 7 0 SHEET 2 AA1 2 ARG A 10 TYR A 12 -1 O TYR A 12 N CYS A 5 SHEET 1 AA2 5 HIS A 34 TYR A 36 0 SHEET 2 AA2 5 PHE A 51 PRO A 55 -1 O GLU A 53 N HIS A 34 SHEET 3 AA2 5 ASP A 70 ASP A 75 -1 O VAL A 72 N TYR A 54 SHEET 4 AA2 5 PHE A 80 THR A 85 -1 O CYS A 81 N ILE A 73 SHEET 5 AA2 5 VAL A 96 GLU A 97 -1 O VAL A 96 N THR A 85 SSBOND 1 CYS A 5 CYS A 83 1555 1555 2.00 SSBOND 2 CYS A 7 CYS A 98 1555 1555 2.07 SSBOND 3 CYS A 47 CYS A 81 1555 1555 2.08 CISPEP 1 TYR A 32 PRO A 33 0 2.80 CRYST1 34.589 46.310 53.524 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 0.028911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018683 0.00000