HEADER HYDROLASE 03-APR-10 3AGN TITLE CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 COMPLEXED TITLE 2 WITH ADENOSINE 3'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE U2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE U2; COMPND 5 EC: 3.1.27.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: USTILAGO SPHAEROGENA; SOURCE 3 ORGANISM_COMMON: SMUT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5271 KEYWDS PURINE-SPECIFIC ENDO-RIBONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NOGUCHI REVDAT 2 04-APR-12 3AGN 1 JRNL VERSN REVDAT 1 07-JUL-10 3AGN 0 JRNL AUTH S.NOGUCHI JRNL TITL ISOMERIZATION MECHANISM OF ASPARTATE TO ISOASPARTATE IMPLIED JRNL TITL 2 BY STRUCTURES OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 JRNL TITL 3 COMPLEXED WITH ADENOSINE 3'-MONOPHOSPHATE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 843 2010 JRNL REFN ISSN 0907-4449 JRNL PMID 20606265 JRNL DOI 10.1107/S0907444910019621 REMARK 2 REMARK 2 RESOLUTION. 0.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 58481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2949 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3571 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2520 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 : 24 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.018 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.018 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.009 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.336 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 982 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 601 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1358 ; 2.405 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1480 ; 3.562 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 122 ; 7.071 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;37.064 ;25.769 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 124 ;12.389 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ; 4.071 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 138 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1143 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 194 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 601 ; 1.122 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 241 ; 0.287 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 972 ; 1.691 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 381 ; 2.160 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 385 ; 2.803 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1582 ; 0.735 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3AGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB029229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 3.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : TRIANGULAR SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58543 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.960 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 14.700 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 72.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.430 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: PDB ENTRY 1RTU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% PEG 8000, 200MM CALCIUM ACETATE, REMARK 280 100MM SODIUM CACODYLATE, 240MM HCL, PH 3.75, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.89450 REMARK 290 SMTRY3 2 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 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 77 86.36 -155.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 116 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 163 O REMARK 620 2 HOH A 164 O 149.7 REMARK 620 3 HOH A 165 O 75.6 78.7 REMARK 620 4 HOH A 166 O 76.1 83.9 79.9 REMARK 620 5 ASP A 50 O 79.4 130.9 137.7 126.0 REMARK 620 6 HOH A 279 O 107.9 86.2 148.4 71.0 72.2 REMARK 620 7 GLN A 112 OE1 111.9 77.9 78.7 154.1 79.8 125.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3AM A 115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 116 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RTU RELATED DB: PDB REMARK 900 THE SAME PROTEIN, ASP45 OF WHICH IS ISOMERIZED TO REMARK 900 ISOASPARTATE REMARK 900 RELATED ID: 3AGO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 REMARK 900 COMPLEXED WITH ADENOSINE 3'-MONOPHOSPHATE DBREF 3AGN 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 ASP 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 3AM A 115 24 HET CA A 116 1 HETNAM 3AM [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2- HETNAM 2 3AM (HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE HETNAM CA CALCIUM ION HETSYN 3AM 3'-AMP FORMUL 2 3AM C10 H14 N5 O7 P FORMUL 3 CA CA 2+ FORMUL 4 HOH *166(H2 O) HELIX 1 1 ASN A 16 ASN A 32 1 17 HELIX 2 2 ARG A 35 TYR A 39 5 5 HELIX 3 3 GLU A 46 ASP A 50 5 5 SHEET 1 A 2 SER A 6 CYS A 9 0 SHEET 2 A 2 ASN A 12 SER A 15 -1 O ASN A 12 N CYS A 9 SHEET 1 B 5 HIS A 41 TYR A 43 0 SHEET 2 B 5 TRP A 60 PRO A 64 -1 O GLU A 62 N HIS A 41 SHEET 3 B 5 ASP A 84 GLN A 89 -1 O TYR A 88 N SER A 61 SHEET 4 B 5 PHE A 95 THR A 100 -1 O ALA A 97 N ILE A 87 SHEET 5 B 5 THR A 111 GLN A 112 -1 O THR A 111 N THR A 100 SSBOND 1 CYS A 1 CYS A 54 1555 1555 2.02 SSBOND 2 CYS A 9 CYS A 113 1555 1555 2.05 SSBOND 3 CYS A 55 CYS A 96 1555 1555 2.03 LINK CA CA A 116 O HOH A 163 1555 1555 2.31 LINK CA CA A 116 O HOH A 164 1555 1555 2.32 LINK CA CA A 116 O HOH A 165 1555 1555 2.35 LINK CA CA A 116 O HOH A 166 1555 1555 2.37 LINK O ASP A 50 CA CA A 116 1555 1555 2.40 LINK CA CA A 116 O HOH A 279 1555 1555 2.51 LINK OE1 GLN A 112 CA CA A 116 1555 1555 2.67 CISPEP 1 TYR A 39 PRO A 40 0 8.00 CISPEP 2 GLY A 58 PRO A 59 0 7.21 CISPEP 3 GLY A 69 PRO A 70 0 5.43 SITE 1 AC1 17 TYR A 39 HIS A 41 GLN A 42 TYR A 43 SITE 2 AC1 17 TYR A 44 GLU A 46 GLU A 49 GLU A 62 SITE 3 AC1 17 ARG A 85 HIS A 101 ASP A 108 PHE A 110 SITE 4 AC1 17 HOH A 180 HOH A 238 HOH A 240 HOH A 246 SITE 5 AC1 17 HOH A 247 SITE 1 AC2 7 ASP A 50 GLN A 112 HOH A 163 HOH A 164 SITE 2 AC2 7 HOH A 165 HOH A 166 HOH A 279 CRYST1 37.880 39.789 35.884 90.00 114.99 90.00 P 1 21 1 2 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 0.026399 0.000000 0.012305 0.00000 SCALE2 0.000000 0.025133 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030746 0.00000