HEADER HYDROLASE(ENDORIBONUCLEASE) 18-JAN-93 1FUS TITLE CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS TITLE 2 FREE FORM AND IN COMPLEX WITH 2'GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE F1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.27.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GIBBERELLA FUJIKUROI; SOURCE 3 ORGANISM_TAXID: 5127 KEYWDS HYDROLASE(ENDORIBONUCLEASE) EXPDTA X-RAY DIFFRACTION AUTHOR K.KATAYANAGI,D.G.VASSYLYEV,K.ISHIKAWA,K.MORIKAWA REVDAT 4 25-DEC-19 1FUS 1 SEQADV SEQRES LINK REVDAT 3 29-NOV-17 1FUS 1 HELIX REVDAT 2 24-FEB-09 1FUS 1 VERSN REVDAT 1 31-OCT-93 1FUS 0 JRNL AUTH D.G.VASSYLYEV,K.KATAYANAGI,K.ISHIKAWA,M.TSUJIMOTO-HIRANO, JRNL AUTH 2 M.DANNO,A.PAHLER,O.MATSUMOTO,M.MATSUSHIMA,H.YOSHIDA, JRNL AUTH 3 K.MORIKAWA JRNL TITL CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM JRNL TITL 2 MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP. JRNL REF J.MOL.BIOL. V. 230 979 1993 JRNL REFN ISSN 0022-2836 JRNL PMID 8386773 JRNL DOI 10.1006/JMBI.1993.1214 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 773 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.015 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.033 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.042 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.015 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.151 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.144 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.164 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.207 ; 0.300 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 2.900 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 15.700; 15.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.023 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.505 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.212 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.299 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FUS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 23.32500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.13000 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 164 O HOH A 175 3544 1.86 REMARK 500 O HOH A 180 O HOH A 191 4444 2.01 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 ARG A 17 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 53 CA - CB - CG ANGL. DEV. = 13.6 DEGREES REMARK 500 GLU A 85 OE1 - CD - OE2 ANGL. DEV. = -8.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE: REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: RFN1_FUSMO REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 999 SER 32 THR 32 REMARK 999 THR 36 SER 36 DBREF 1FUS A 2 107 UNP P10282 RNF1_GIBFU 2 106 SEQADV 1FUS THR A 32 UNP P10282 SER 32 CONFLICT SEQADV 1FUS SER A 36 UNP P10282 THR 36 CONFLICT SEQRES 1 A 106 PCA SER ALA THR THR CYS GLY SER THR ASN TYR SER ALA SEQRES 2 A 106 SER GLN VAL ARG ALA ALA ALA ASN ALA ALA CYS GLN TYR SEQRES 3 A 106 TYR GLN ASN ASP ASP THR ALA GLY SER SER THR TYR PRO SEQRES 4 A 106 HIS THR TYR ASN ASN TYR GLU GLY PHE ASP PHE PRO VAL SEQRES 5 A 106 ASP GLY PRO TYR GLN GLU PHE PRO ILE LYS SER GLY GLY SEQRES 6 A 106 VAL TYR THR GLY GLY SER PRO GLY ALA ASP ARG VAL VAL SEQRES 7 A 106 ILE ASN THR ASN CYS GLU TYR ALA GLY ALA ILE THR HIS SEQRES 8 A 106 THR GLY ALA SER GLY ASN ASN PHE VAL GLY CYS SER GLY SEQRES 9 A 106 THR ASN MODRES 1FUS PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 FORMUL 2 HOH *107(H2 O) HELIX 1 1 ALA A 13 GLN A 28 1 16 SHEET 1 S1 2 ALA A 3 CYS A 6 0 SHEET 2 S1 2 THR A 9 SER A 12 -1 O TYR A 11 N THR A 4 SHEET 1 S2 5 TYR A 38 TYR A 42 0 SHEET 2 S2 5 ASP A 53 LYS A 62 -1 O GLU A 58 N HIS A 40 SHEET 3 S2 5 ASP A 76 THR A 82 -1 N THR A 82 O PRO A 55 SHEET 4 S2 5 GLY A 88 THR A 91 -1 O ILE A 90 N ARG A 77 SHEET 5 S2 5 VAL A 101 CYS A 103 -1 N CYS A 103 O ALA A 89 SSBOND 1 CYS A 6 CYS A 103 1555 1555 2.04 SSBOND 2 CYS A 24 CYS A 84 1555 1555 2.06 LINK C PCA A 1 N SER A 2 1555 1555 1.33 CISPEP 1 TYR A 38 PRO A 39 0 -4.75 CISPEP 2 GLY A 54 PRO A 55 0 -0.36 CRYST1 46.650 56.260 31.600 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 0.021436 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031646 0.00000 HETATM 1 N PCA A 1 4.631 -20.560 -11.920 1.00 28.76 N HETATM 2 CA PCA A 1 5.694 -20.702 -10.956 1.00 27.22 C HETATM 3 CB PCA A 1 5.386 -19.668 -9.875 1.00 28.81 C HETATM 4 CG PCA A 1 3.903 -19.322 -10.105 1.00 29.06 C HETATM 5 CD PCA A 1 3.805 -19.534 -11.614 1.00 29.29 C HETATM 6 OE PCA A 1 3.141 -18.888 -12.432 1.00 30.56 O HETATM 7 C PCA A 1 5.760 -22.087 -10.307 1.00 26.37 C HETATM 8 O PCA A 1 4.925 -22.973 -10.427 1.00 25.40 O