HEADER COMPLEX (HYDROLASE/CYTIDYLIC ACID) 08-NOV-95 1RNN TITLE RIBONUCLEASE A COMPLEX WITH CYTIDYLIC ACID (5'CMP) CRYSTALLIZED FROM TITLE 2 8M SODIUM FORMATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE A; COMPND 3 CHAIN: E; COMPND 4 SYNONYM: RNASE A/5'-CMP; COMPND 5 EC: 3.1.27.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: PANCREAS KEYWDS COMPLEX (HYDROLASE-CYTIDYLIC ACID), COMPLEX (HYDROLASE-CYTIDYLIC KEYWDS 2 ACID) COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,S.C.ALMO REVDAT 4 14-AUG-19 1RNN 1 REMARK REVDAT 3 17-JUL-19 1RNN 1 REMARK REVDAT 2 24-FEB-09 1RNN 1 VERSN REVDAT 1 03-APR-96 1RNN 0 JRNL AUTH A.A.FEDOROV,D.JOSEF-MCCARTHY,I.GRAF,D.ANGUELOVA,E.V.FEDOROV, JRNL AUTH 2 S.C.ALMO JRNL TITL STRUCTURE OF THE CRYSTALLINE COMPLEX OF BOVINE PANCREATIC JRNL TITL 2 RIBONUCLEASE A AND CYTIDYLIC ACID JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL 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)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12259 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 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 : 951 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 103 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) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RNN 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_1000176141. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1993 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS-NICOLET X100 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 9.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 200 DATA REDUNDANCY : 2.520 REMARK 200 R MERGE (I) : 0.04100 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) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.51 REMARK 200 R MERGE FOR SHELL (I) : 0.26100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.930 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.51467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.75733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.75733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.51467 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: E 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 HIS E 48 59.67 -104.33 REMARK 500 GLN E 60 -140.33 -103.86 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 C5P E 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT E 131 DBREF 1RNN E 1 124 UNP P61823 RNAS1_BOVIN 27 150 SEQRES 1 E 124 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 E 124 ASP SER SER THR SER ALA ALA SER SER SER ASN TYR CYS SEQRES 3 E 124 ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP ARG SEQRES 4 E 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 E 124 ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS SEQRES 6 E 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER THR SEQRES 7 E 124 MET SER ILE THR ASP CYS ARG GLU THR GLY SER SER LYS SEQRES 8 E 124 TYR PRO ASN CYS ALA TYR LYS THR THR GLN ALA ASN LYS SEQRES 9 E 124 HIS ILE ILE VAL ALA CYS GLU GLY ASN PRO TYR VAL PRO SEQRES 10 E 124 VAL HIS PHE ASP ALA SER VAL HET C5P E 200 21 HET FMT E 131 3 HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETNAM FMT FORMIC ACID FORMUL 2 C5P C9 H14 N3 O8 P FORMUL 3 FMT C H2 O2 FORMUL 4 HOH *103(H2 O) HELIX 1 H1 THR E 3 MET E 13 1 11 HELIX 2 H2 ASN E 24 ASN E 34 1RESIDUE 34 IN 3/10 CONFIG 11 HELIX 3 H3 SER E 50 GLN E 60 1RESIDUES 56-60 IN 3/10 CONFIG 11 SHEET 1 S1A 3 LYS E 41 HIS E 48 0 SHEET 2 S1A 3 MET E 79 THR E 87 -1 N GLU E 86 O PRO E 42 SHEET 3 S1A 3 ASN E 94 LYS E 104 -1 O LYS E 104 N MET E 79 SHEET 1 S1B 3 LYS E 41 HIS E 48 0 SHEET 2 S1B 3 SER E 90 LYS E 91 -1 SHEET 3 S1B 3 ASN E 94 LYS E 104 -1 O ASN E 94 N LYS E 91 SHEET 1 S2A 4 LYS E 61 ALA E 64 0 SHEET 2 S2A 4 ASN E 71 SER E 75 -1 O CYS E 72 N VAL E 63 SHEET 3 S2A 4 HIS E 105 ASN E 113 -1 O VAL E 108 N TYR E 73 SHEET 4 S2A 4 PRO E 114 HIS E 119 -1 O VAL E 116 N GLU E 111 SHEET 1 S2B 4 LYS E 61 ALA E 64 0 SHEET 2 S2B 4 ASN E 71 SER E 75 -1 O CYS E 72 N VAL E 63 SHEET 3 S2B 4 HIS E 105 ASN E 113 -1 O VAL E 108 N TYR E 73 SHEET 4 S2B 4 ASP E 121 VAL E 124 -1 N VAL E 124 O HIS E 105 SSBOND 1 CYS E 26 CYS E 84 1555 1555 2.02 SSBOND 2 CYS E 40 CYS E 95 1555 1555 1.99 SSBOND 3 CYS E 58 CYS E 110 1555 1555 1.97 SSBOND 4 CYS E 65 CYS E 72 1555 1555 2.03 CISPEP 1 TYR E 92 PRO E 93 0 2.36 CISPEP 2 ASN E 113 PRO E 114 0 0.19 SITE 1 AC1 10 HIS E 12 LYS E 41 VAL E 43 ASN E 44 SITE 2 AC1 10 THR E 45 HIS E 119 PHE E 120 FMT E 131 SITE 3 AC1 10 HOH E 255 HOH E 262 SITE 1 AC2 5 GLN E 11 HIS E 12 HIS E 119 PHE E 120 SITE 2 AC2 5 C5P E 200 CRYST1 65.114 65.114 65.272 90.00 90.00 120.00 P 32 2 1 6 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 0.015358 0.008867 0.000000 0.00000 SCALE2 0.000000 0.017734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015321 0.00000