HEADER RIBONUCLEASE INHIBITOR 25-DEC-97 1A19 TITLE BARSTAR (FREE), C82A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BARSTAR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS AMYLOLIQUEFACIENS; SOURCE 3 ORGANISM_TAXID: 1390; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BARSTAR, C82A, DIMER, UNCOMPLEXED, RIBONUCLEASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR G.S.RATNAPARKHI,R.VARADARAJAN REVDAT 4 02-AUG-23 1A19 1 REMARK REVDAT 3 03-NOV-21 1A19 1 SEQADV REVDAT 2 24-FEB-09 1A19 1 VERSN REVDAT 1 08-APR-98 1A19 0 JRNL AUTH G.S.RATNAPARKHI,S.RAMACHANDRAN,J.B.UDGAONKAR,R.VARADARAJAN JRNL TITL DISCREPANCIES BETWEEN THE NMR AND X-RAY STRUCTURES OF JRNL TITL 2 UNCOMPLEXED BARSTAR: ANALYSIS SUGGESTS THAT PACKING JRNL TITL 3 DENSITIES OF PROTEIN STRUCTURES DETERMINED BY NMR ARE JRNL TITL 4 UNRELIABLE. JRNL REF BIOCHEMISTRY V. 37 6958 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9578582 JRNL DOI 10.1021/BI972857N REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0100 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 4081 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 SET) : 0.203 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 15.100 REMARK 3 FREE R VALUE TEST SET COUNT : 618 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 226 REMARK 3 BIN R VALUE (WORKING SET) : 0.4650 REMARK 3 BIN FREE R VALUE : 0.4650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 33 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.081 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1438 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.40 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) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.57 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) : 0.52 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.540 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 NCS MODEL : RESTRAINED, 100 KCAL/MOL WEIGHT FINAL POSITIONAL REMARK 3 REFINEMENT USING ALL REFLECTIONS AND REMOVING NCS REMARK 3 RESTRAINTS. 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MET PRESENT AT N-TERMINUS DURING REMARK 3 EXPRESSION IS NOT INCLUDED IN THE SEQUENCE OR THE STRUCTURE. REMARK 4 REMARK 4 1A19 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_1000170267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MARXDS REMARK 200 DATA SCALING SOFTWARE : MARSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4796 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.760 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.05000 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRIES 1BGS, 1BRS REMARK 200 REMARK 200 REMARK: 1BGS & 2BRS ARE THE COMPLEX OF BARSTAR WITH BARNASE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: C82A MUTANT WAS CRYSTALLIZED FROM 40 REMARK 280 -60% AMMONIUM SULFATE, 50MM PHOSPHATE, PH=6.5. PROTEIN CONC=45 REMARK 280 MG/ML. C40A AND DTNB LABELLED CRYSTALS ALSO CRYSTALLIZED BUT DID REMARK 280 NOT DIFFRACT TO HIGH RESOLUTION., PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 52.09100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 52.09100 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.09100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 9.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.09100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 52.09100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.09100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 52.09100 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 27.00000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 52.09100 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 9.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 0 REMARK 465 MET B 0 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 ILE A 10 76.17 -66.87 REMARK 500 LEU A 26 172.64 -58.41 REMARK 500 TYR A 30 115.19 -39.82 REMARK 500 SER A 59 -16.39 -47.16 REMARK 500 LEU A 62 33.12 -76.43 REMARK 500 THR A 63 23.68 -155.08 REMARK 500 ALA A 82 139.87 -36.85 REMARK 500 ILE B 10 77.28 -69.57 REMARK 500 LEU B 26 176.18 -54.34 REMARK 500 TYR B 30 107.79 -38.75 REMARK 500 LEU B 62 30.31 -79.07 REMARK 500 THR B 63 23.21 -152.09 REMARK 500 ALA B 82 139.74 -35.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A19 A 1 89 UNP P11540 BARS_BACAM 1 89 DBREF 1A19 B 1 89 UNP P11540 BARS_BACAM 1 89 SEQADV 1A19 ALA A 82 UNP P11540 CYS 82 ENGINEERED MUTATION SEQADV 1A19 ALA B 82 UNP P11540 CYS 82 ENGINEERED MUTATION SEQRES 1 A 90 MET LYS LYS ALA VAL ILE ASN GLY GLU GLN ILE ARG SER SEQRES 2 A 90 ILE SER ASP LEU HIS GLN THR LEU LYS LYS GLU LEU ALA SEQRES 3 A 90 LEU PRO GLU TYR TYR GLY GLU ASN LEU ASP ALA LEU TRP SEQRES 4 A 90 ASP CYS LEU THR GLY TRP VAL GLU TYR PRO LEU VAL LEU SEQRES 5 A 90 GLU TRP ARG GLN PHE GLU GLN SER LYS GLN LEU THR GLU SEQRES 6 A 90 ASN GLY ALA GLU SER VAL LEU GLN VAL PHE ARG GLU ALA SEQRES 7 A 90 LYS ALA GLU GLY ALA ASP ILE THR ILE ILE LEU SER SEQRES 1 B 90 MET LYS LYS ALA VAL ILE ASN GLY GLU GLN ILE ARG SER SEQRES 2 B 90 ILE SER ASP LEU HIS GLN THR LEU LYS LYS GLU LEU ALA SEQRES 3 B 90 LEU PRO GLU TYR TYR GLY GLU ASN LEU ASP ALA LEU TRP SEQRES 4 B 90 ASP CYS LEU THR GLY TRP VAL GLU TYR PRO LEU VAL LEU SEQRES 5 B 90 GLU TRP ARG GLN PHE GLU GLN SER LYS GLN LEU THR GLU SEQRES 6 B 90 ASN GLY ALA GLU SER VAL LEU GLN VAL PHE ARG GLU ALA SEQRES 7 B 90 LYS ALA GLU GLY ALA ASP ILE THR ILE ILE LEU SER HELIX 1 1 ILE A 13 GLU A 23 1 11 HELIX 2 2 LEU A 34 LEU A 41 1 8 HELIX 3 3 PHE A 56 THR A 63 1 8 HELIX 4 4 ALA A 67 GLU A 80 1 14 HELIX 5 5 ILE B 13 GLU B 23 1 11 HELIX 6 6 LEU B 34 LEU B 41 1 8 HELIX 7 7 PHE B 56 THR B 63 1 8 HELIX 8 8 ALA B 67 GLU B 80 1 14 SHEET 1 A 3 LYS A 2 ASN A 6 0 SHEET 2 A 3 LEU A 49 ARG A 54 1 N VAL A 50 O ALA A 3 SHEET 3 A 3 ILE A 84 ILE A 87 1 N THR A 85 O LEU A 49 SHEET 1 B 3 LYS B 2 ASN B 6 0 SHEET 2 B 3 LEU B 49 ARG B 54 1 N VAL B 50 O ALA B 3 SHEET 3 B 3 ILE B 84 ILE B 87 1 N THR B 85 O LEU B 49 CISPEP 1 TYR A 47 PRO A 48 0 0.04 CISPEP 2 TYR B 47 PRO B 48 0 -0.30 CRYST1 104.182 104.182 36.000 90.00 90.00 90.00 I 41 16 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 0.009599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027778 0.00000