HEADER HYDROLASE 29-NOV-01 1KH8 TITLE STRUCTURE OF A CIS-PROLINE (P114) TO GLYCINE VARIANT OF RIBONUCLEASE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANCREATIC RIBONUCLEASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEASE PANCREATIC, RNASE 1, RNASE A; COMPND 5 EC: 3.1.27.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASE A, RIBONUCLEASE A, PROLINE, CIS, TRANS, CESIUM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.A.SCHULTZ,A.M.FRIEDMAN,M.A.WHITE,R.O.FOX REVDAT 5 03-APR-24 1KH8 1 REMARK REVDAT 4 27-OCT-21 1KH8 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1KH8 1 VERSN REVDAT 2 08-NOV-05 1KH8 1 JRNL REVDAT 1 17-JUN-03 1KH8 0 JRNL AUTH D.A.SCHULTZ,A.M.FRIEDMAN,M.A.WHITE,R.O.FOX JRNL TITL THE CRYSTAL STRUCTURE OF THE CIS-PROLINE TO GLYCINE VARIANT JRNL TITL 2 (P114G) OF RIBONUCLEASE A. JRNL REF PROTEIN SCI. V. 14 2862 2005 JRNL REFN ISSN 0961-8368 JRNL PMID 16199662 JRNL DOI 10.1110/PS.051610505 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 7592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT CNS REFINEMENT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 397 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 12 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.073 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 956 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.43000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.610 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR REFINEMENT (6-2A) USED FOR REMARK 3 INITIAL MODEL BUILDING WITHOUT CV SET. FINAL ROUNDS OF MODEL REMARK 3 BUILDING (30-2A) WERE PERFORMED IN CNS WITH A 5% CV SET AND REMARK 3 SEVERAL ROUNDS OF SIMULATED ANNEALING TO REMOVE BIAS. WATERS REMARK 3 WERE PICKED USING CNS AFTER SA REFINEMENT. THE SIGMA WEIGHTED R- REMARK 3 FACTOR (RW) ON ALL REFLECTIONS IS 18.0%. REMARK 4 REMARK 4 1KH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 6.6 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.8 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: HIGH SALT WILD TYPE RNASE A (PAUL: KIM, ET AL, REMARK 200 BIOCHEMISTRY 1992,31,12304-12314) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAPO4, CSCL2, AMMONIUM SULFATE, PH REMARK 280 6.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.62500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.43500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 96.93750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.43500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.43500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.31250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.43500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.43500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 96.93750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.43500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.43500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.31250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.62500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 186 LIES ON A SPECIAL POSITION. 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 ARG A 39 171.79 160.52 REMARK 500 HIS A 48 61.99 -102.43 REMARK 500 GLN A 60 -135.70 -107.70 REMARK 500 LYS A 91 109.40 -162.68 REMARK 500 ALA A 122 -179.57 -178.75 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 CS A 126 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 58 O REMARK 620 2 TYR A 73 OH 91.0 REMARK 620 3 ASN A 113 O 141.2 83.8 REMARK 620 4 GLY A 114 O 87.9 114.7 60.3 REMARK 620 N 1 2 3 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 125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS A 126 DBREF 1KH8 A 1 124 UNP P61823 RNAS1_BOVIN 27 150 SEQADV 1KH8 MET A 0 UNP P61823 INITIATING METHIONINE SEQADV 1KH8 GLY A 114 UNP P61823 PRO 140 ENGINEERED MUTATION SEQRES 1 A 125 MET LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS SEQRES 2 A 125 MET ASP SER SER THR SER ALA ALA SER SER SER ASN TYR SEQRES 3 A 125 CYS ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP SEQRES 4 A 125 ARG CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU SEQRES 5 A 125 ALA ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA SEQRES 6 A 125 CYS LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER SEQRES 7 A 125 THR MET SER ILE THR ASP CYS ARG GLU THR GLY SER SER SEQRES 8 A 125 LYS TYR PRO ASN CYS ALA TYR LYS THR THR GLN ALA ASN SEQRES 9 A 125 LYS HIS ILE ILE VAL ALA CYS GLU GLY ASN GLY TYR VAL SEQRES 10 A 125 PRO VAL HIS PHE ASP ALA SER VAL HET SO4 A 125 5 HET CS A 126 1 HETNAM SO4 SULFATE ION HETNAM CS CESIUM ION FORMUL 2 SO4 O4 S 2- FORMUL 3 CS CS 1+ FORMUL 4 HOH *62(H2 O) HELIX 1 1 THR A 3 MET A 13 1 11 HELIX 2 2 ASN A 24 ARG A 33 1 10 HELIX 3 3 SER A 50 ALA A 56 1 7 HELIX 4 4 VAL A 57 GLN A 60 5 4 HELIX 5 5 GLY A 112 GLY A 114 5 3 SHEET 1 A 5 VAL A 43 VAL A 47 0 SHEET 2 A 5 MET A 79 GLU A 86 -1 O THR A 82 N PHE A 46 SHEET 3 A 5 TYR A 97 CYS A 110 -1 O LYS A 104 N MET A 79 SHEET 4 A 5 CYS A 72 GLN A 74 -1 N TYR A 73 O VAL A 108 SHEET 5 A 5 LYS A 61 VAL A 63 -1 N LYS A 61 O GLN A 74 SHEET 1 B 4 VAL A 43 VAL A 47 0 SHEET 2 B 4 MET A 79 GLU A 86 -1 O THR A 82 N PHE A 46 SHEET 3 B 4 TYR A 97 CYS A 110 -1 O LYS A 104 N MET A 79 SHEET 4 B 4 PRO A 117 VAL A 124 -1 O VAL A 124 N HIS A 105 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.03 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.03 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.03 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.03 LINK O CYS A 58 CS CS A 126 1555 1555 2.94 LINK OH TYR A 73 CS CS A 126 1555 1555 3.09 LINK O ASN A 113 CS CS A 126 1555 1555 3.14 LINK O GLY A 114 CS CS A 126 1555 1555 3.02 CISPEP 1 TYR A 92 PRO A 93 0 0.17 SITE 1 AC1 5 GLN A 11 HIS A 12 LYS A 41 HIS A 119 SITE 2 AC1 5 PHE A 120 SITE 1 AC2 4 CYS A 58 TYR A 73 ASN A 113 GLY A 114 CRYST1 40.870 40.870 129.250 90.00 90.00 90.00 P 43 21 2 8 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 0.024468 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007737 0.00000