HEADER HYDROLASE 15-JUL-99 1C0C TITLE BOVINE PANCREATIC RIBONUCLEASE A DESICCATED FOR 4.0 DAYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE A; COMPND 3 CHAIN: A; COMPND 4 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 HYDROLASE (PHOSPHORIC DIESTER, RNA), DESICCATED, DRY, DEHYDRATED, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.BELL REVDAT 4 30-OCT-24 1C0C 1 REMARK REVDAT 3 04-OCT-17 1C0C 1 REMARK REVDAT 2 24-FEB-09 1C0C 1 VERSN REVDAT 1 14-OCT-99 1C0C 0 JRNL AUTH J.A.BELL JRNL TITL X-RAY CRYSTAL STRUCTURES OF A SEVERELY DESICCATED PROTEIN JRNL REF PROTEIN SCI. V. 8 2033 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10548049 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 3 NUMBER OF REFLECTIONS : 4363 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 413 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. 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 : 15 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 41.000 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.270 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FINAL FIVE CYCLES OF REFINEMENT REMARK 3 INCLUDED ALL OBSERVED DATA REMARK 4 REMARK 4 1C0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4742 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19000 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: NULL REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 58% METHANOL (V/V), PH 4.5, SMALL REMARK 280 TUBES, TEMPERATURE 295K 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 17.85000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.85000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A -3 REMARK 465 SER A -2 REMARK 465 LEU A -1 REMARK 465 GLY A 0 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 GLU A 111 CD GLU A 111 OE2 0.066 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 ASP A 83 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 121 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 THR A 3 -25.87 -171.63 REMARK 500 ASP A 14 73.36 -151.36 REMARK 500 SER A 15 58.68 -94.34 REMARK 500 ALA A 19 -159.89 -143.87 REMARK 500 ALA A 20 107.47 -162.19 REMARK 500 SER A 22 149.78 160.15 REMARK 500 TYR A 25 -73.01 -38.51 REMARK 500 ASP A 38 -68.30 73.69 REMARK 500 SER A 50 137.10 -39.99 REMARK 500 GLN A 60 -126.66 -138.33 REMARK 500 LYS A 66 35.21 -83.09 REMARK 500 ASN A 67 -97.30 -159.51 REMARK 500 GLN A 69 -170.35 142.69 REMARK 500 THR A 70 149.52 -8.95 REMARK 500 ASN A 71 5.37 96.25 REMARK 500 SER A 77 -133.55 -99.63 REMARK 500 SER A 89 134.28 96.96 REMARK 500 SER A 90 107.93 125.87 REMARK 500 LYS A 91 76.30 -65.19 REMARK 500 TYR A 92 -177.30 -175.03 REMARK 500 PRO A 93 -6.96 -43.69 REMARK 500 ASN A 113 -24.51 176.61 REMARK 500 ASP A 121 -128.95 -75.55 REMARK 500 SER A 123 63.65 -104.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 113 PRO A 114 38.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 113 12.39 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 SO4 A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 152 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BEL RELATED DB: PDB REMARK 900 SAME CRYSTAL FORM, FULLY SOLVATED DBREF 1C0C A -3 124 UNP P61823 RNAS1_BOVIN 1 128 SEQRES 1 A 128 PRO SER LEU GLY LYS GLU THR ALA ALA ALA LYS PHE GLU SEQRES 2 A 128 ARG GLN HIS MET ASP SER SER THR SER ALA ALA SER SER SEQRES 3 A 128 SER ASN TYR CYS ASN GLN MET MET LYS SER ARG ASN LEU SEQRES 4 A 128 THR LYS ASP ARG CYS LYS PRO VAL ASN THR PHE VAL HIS SEQRES 5 A 128 GLU SER LEU ALA ASP VAL GLN ALA VAL CYS SER GLN LYS SEQRES 6 A 128 ASN VAL ALA CYS LYS ASN GLY GLN THR ASN CYS TYR GLN SEQRES 7 A 128 SER TYR SER THR MET SER ILE THR ASP CYS ARG GLU THR SEQRES 8 A 128 GLY SER SER LYS TYR PRO ASN CYS ALA TYR LYS THR THR SEQRES 9 A 128 GLN ALA ASN LYS HIS ILE ILE VAL ALA CYS GLU GLY ASN SEQRES 10 A 128 PRO TYR VAL PRO VAL HIS PHE ASP ALA SER VAL HET SO4 A 150 5 HET SO4 A 151 5 HET SO4 A 152 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *2(H2 O) HELIX 1 1 THR A 3 MET A 13 1 11 HELIX 2 2 SER A 22 ARG A 33 1 12 HELIX 3 3 SER A 50 VAL A 57 1 8 HELIX 4 4 CYS A 58 GLN A 60 5 3 SHEET 1 A 3 VAL A 43 VAL A 47 0 SHEET 2 A 3 MET A 79 THR A 87 -1 O THR A 82 N PHE A 46 SHEET 3 A 3 ALA A 96 LYS A 104 -1 O ALA A 96 N THR A 87 SHEET 1 B 4 LYS A 61 VAL A 63 0 SHEET 2 B 4 CYS A 72 GLN A 74 -1 O CYS A 72 N VAL A 63 SHEET 3 B 4 ILE A 107 GLU A 111 -1 O VAL A 108 N TYR A 73 SHEET 4 B 4 VAL A 116 PHE A 120 -1 O VAL A 116 N GLU A 111 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.01 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.02 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.02 SSBOND 4 CYS A 65 CYS A 72 1555 1555 1.96 SITE 1 AC1 9 SER A 15 SER A 22 SER A 23 SER A 50 SITE 2 AC1 9 LEU A 51 LYS A 61 TYR A 76 LYS A 91 SITE 3 AC1 9 THR A 99 SITE 1 AC2 8 LYS A 7 GLN A 11 HIS A 12 LYS A 31 SITE 2 AC2 8 VAL A 118 HIS A 119 PHE A 120 HOH A 201 SITE 1 AC3 9 HIS A 12 LYS A 31 LYS A 41 VAL A 43 SITE 2 AC3 9 ASN A 44 THR A 45 GLY A 112 ASN A 113 SITE 3 AC3 9 PRO A 114 CRYST1 35.700 39.700 50.800 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 0.028011 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019685 0.00000