HEADER HYDROLASE 12-MAY-95 1RTU TITLE USTILAGO SPHAEROGENA RIBONUCLEASE U2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE U2; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: USTILAGO SPHAEROGENA; SOURCE 3 ORGANISM_TAXID: 5271; SOURCE 4 ATCC: 12421 KEYWDS HYDROLASE, ENDORIBONUCLEASE, BETA-ISOMERIZED ASPARTATE EXPDTA X-RAY DIFFRACTION AUTHOR S.NOGUCHI,Y.SATOW,T.UCHIDA,C.SASAKI,T.MATSUZAKI REVDAT 9 13-NOV-24 1RTU 1 REMARK REVDAT 8 09-AUG-23 1RTU 1 REMARK LINK REVDAT 7 04-APR-18 1RTU 1 REMARK REVDAT 6 27-JUL-11 1RTU 1 HETNAM HETSYN REMARK REVDAT 5 13-JUL-11 1RTU 1 VERSN REVDAT 4 14-APR-10 1RTU 1 ATOM REVDAT 3 08-SEP-09 1RTU 1 HET REVDAT 2 24-FEB-09 1RTU 1 VERSN REVDAT 1 08-NOV-96 1RTU 0 JRNL AUTH S.NOGUCHI,Y.SATOW,T.UCHIDA,C.SASAKI,T.MATSUZAKI JRNL TITL CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 AT JRNL TITL 2 1.8 A RESOLUTION. JRNL REF BIOCHEMISTRY V. 34 15583 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7492561 JRNL DOI 10.1021/BI00047A025 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 9807 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) : NULL 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) : 0.1430 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1410 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9807 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 870 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.40 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.13 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) : 0.014 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.028 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.041 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.014 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.170 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.157 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.147 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.173 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 2.600 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 12.400; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 25.200; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.760 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.214 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.730 ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.720 ; 2.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RTU 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_1000176226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-90 REMARK 200 TEMPERATURE (KELVIN) : 284 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : DOUBLE FOCUSSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : TOMOKO, MARIKO (LOCAL PROGRAM), REMARK 200 OSC (LOCAL VERSION) REMARK 200 DATA SCALING SOFTWARE : A PROGRAM BY TOMOKO, MARIKO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.03420 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.07700 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: RNASE T1 (PDB ENTRY 1RNT) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE PREPARED BY HANGING-DROP REMARK 280 VAPOUR-DIFFUSION METHOD AT 293 KELVIN FROM A 20 MG/ML PROTEIN REMARK 280 SOLUTION CONTAINING 15 MG/ML 2'-DEOXY 2'-FLUORO ADENYLYL-3',5'- REMARK 280 CYTIDINE, 0.4M AMMONIUM SULFATE, EQUILIBRATED AGAINST A REMARK 280 RESERVOIR OF 0.9M AMMONIUM SULFATE CONTAINING 0.1M ACETATE REMARK 280 BUFFER (PH 4.5)., VAPOR DIFFUSION - HANGING DROP, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 24.66000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.47500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.47500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.66000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.63500 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 400 REMARK 400 COMPOUND REMARK 400 ASP 45 IS ISOMERIZED TO L-ISOASPARTATE. A PEPTIDE REMARK 400 BOND IS FORMED BETWEEN ASP 45 CG AND GLU 46 N. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 5 CD OE1 NE2 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 392 O HOH A 431 2565 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 DBREF 1RTU A 1 114 UNP P00654 RNU2_USTSP 1 114 SEQRES 1 A 114 CYS ASP ILE PRO GLN SER THR ASN CYS GLY GLY ASN VAL SEQRES 2 A 114 TYR SER ASN ASP ASP ILE ASN THR ALA ILE GLN GLY ALA SEQRES 3 A 114 LEU ASP ASP VAL ALA ASN GLY ASP ARG PRO ASP ASN TYR SEQRES 4 A 114 PRO HIS GLN TYR TYR IAS GLU ALA SER GLU ASP ILE THR SEQRES 5 A 114 LEU CYS CYS GLY SER GLY PRO TRP SER GLU PHE PRO LEU SEQRES 6 A 114 VAL TYR ASN GLY PRO TYR TYR SER SER ARG ASP ASN TYR SEQRES 7 A 114 VAL SER PRO GLY PRO ASP ARG VAL ILE TYR GLN THR ASN SEQRES 8 A 114 THR GLY GLU PHE CYS ALA THR VAL THR HIS THR GLY ALA SEQRES 9 A 114 ALA SER TYR ASP GLY PHE THR GLN CYS SER HET IAS A 45 8 HET SO4 A 201 5 HETNAM IAS BETA-L-ASPARTIC ACID HETNAM SO4 SULFATE ION HETSYN IAS L-ASPARTIC ACID FORMUL 1 IAS C4 H7 N O4 FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *141(H2 O) HELIX 1 1 ASN A 16 ASN A 32 1 17 HELIX 2 2 PRO A 36 ASN A 38 5 3 SHEET 1 A 2 SER A 6 CYS A 9 0 SHEET 2 A 2 ASN A 12 SER A 15 -1 N TYR A 14 O THR A 7 SHEET 1 B 4 HIS A 41 TYR A 43 0 SHEET 2 B 4 TRP A 60 PRO A 64 -1 N GLU A 62 O HIS A 41 SHEET 3 B 4 ASP A 84 GLN A 89 -1 N TYR A 88 O SER A 61 SHEET 4 B 4 PHE A 95 THR A 100 -1 N VAL A 99 O ARG A 85 SSBOND 1 CYS A 1 CYS A 54 1555 1555 2.07 SSBOND 2 CYS A 9 CYS A 113 1555 1555 2.04 SSBOND 3 CYS A 55 CYS A 96 1555 1555 2.00 LINK C TYR A 44 N IAS A 45 1555 1555 1.30 LINK CG IAS A 45 N GLU A 46 1555 1555 1.35 CISPEP 1 TYR A 39 PRO A 40 0 -3.98 CISPEP 2 GLY A 58 PRO A 59 0 0.88 CISPEP 3 GLY A 69 PRO A 70 0 1.45 SITE 1 CAT 5 TYR A 39 HIS A 41 GLU A 62 ARG A 85 SITE 2 CAT 5 HIS A 101 SITE 1 AC1 7 TYR A 39 HIS A 41 GLU A 62 ARG A 85 SITE 2 AC1 7 HIS A 101 PHE A 110 HOH A 396 CRYST1 49.320 61.270 34.950 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 0.020276 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028612 0.00000