HEADER HYDROLASE INHIBITOR 06-NOV-98 2UGI TITLE PROTEIN MIMICRY OF DNA FROM CRYSTAL STRUCTURES OF THE URACIL TITLE 2 GLYCOSYLASE INHIBITOR PROTEIN AND ITS COMPLEX WITH ESCHERICHIA COLI TITLE 3 URACIL-DNA GLYCOSYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE INHIBITOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UGI; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PBS2; SOURCE 3 ORGANISM_TAXID: 10684; SOURCE 4 CELLULAR_LOCATION: CYTOPLASM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PKK223-3; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PZWTAC1; SOURCE 12 EXPRESSION_SYSTEM_GENE: TAC KEYWDS PROTEIN MIMICRY OF DNA, PROTEIN INHIBITOR, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR C.D.PUTNAM,A.S.ARVAI,C.D.MOL,J.A.TAINER REVDAT 6 03-APR-24 2UGI 1 REMARK REVDAT 5 27-DEC-23 2UGI 1 REMARK REVDAT 4 24-FEB-09 2UGI 1 VERSN REVDAT 3 01-MAR-05 2UGI 1 HEADER DBREF HETATM REMARK REVDAT 2 01-APR-03 2UGI 1 JRNL REVDAT 1 25-MAR-99 2UGI 0 JRNL AUTH C.D.PUTNAM,M.J.SHROYER,A.J.LUNDQUIST,C.D.MOL,A.S.ARVAI, JRNL AUTH 2 D.W.MOSBAUGH,J.A.TAINER JRNL TITL PROTEIN MIMICRY OF DNA FROM CRYSTAL STRUCTURES OF THE JRNL TITL 2 URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN AND ITS COMPLEX JRNL TITL 3 WITH ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE JRNL REF J.MOL.BIOL. V. 287 331 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10080896 JRNL DOI 10.1006/JMBI.1999.2605 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 9435 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) : 0.227 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 958 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1081 REMARK 3 BIN R VALUE (WORKING SET) : 0.3620 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 95 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.34000 REMARK 3 B22 (A**2) : 5.64300 REMARK 3 B33 (A**2) : 2.70000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.250 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) : 1.556 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.724 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.417 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.888 ; 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2UGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000043. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9507 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25100 REMARK 200 FOR SHELL : 6.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: UGI FROM THE HUMAN UDG:UGI CRYSTAL STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, IMIDAZOLE, MALATE, REMARK 280 (NH4)2SO4, PH 8.2, TEMPERATURE 293.0K 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 21.04600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.79150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.69350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.79150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.04600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.69350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 1 REMARK 465 MET B 1 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 SER B 39 -164.90 -119.21 REMARK 500 ASP B 52 50.67 71.08 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 IMD A 1500 DBREF 2UGI A 1 84 UNP P14739 UNGI_BPPB2 1 84 DBREF 2UGI B 1 84 UNP P14739 UNGI_BPPB2 1 84 SEQRES 1 A 84 MET THR ASN LEU SER ASP ILE ILE GLU LYS GLU THR GLY SEQRES 2 A 84 LYS GLN LEU VAL ILE GLN GLU SER ILE LEU MET LEU PRO SEQRES 3 A 84 GLU GLU VAL GLU GLU VAL ILE GLY ASN LYS PRO GLU SER SEQRES 4 A 84 ASP ILE LEU VAL HIS THR ALA TYR ASP GLU SER THR ASP SEQRES 5 A 84 GLU ASN VAL MET LEU LEU THR SER ASP ALA PRO GLU TYR SEQRES 6 A 84 LYS PRO TRP ALA LEU VAL ILE GLN ASP SER ASN GLY GLU SEQRES 7 A 84 ASN LYS ILE LYS MET LEU SEQRES 1 B 84 MET THR ASN LEU SER ASP ILE ILE GLU LYS GLU THR GLY SEQRES 2 B 84 LYS GLN LEU VAL ILE GLN GLU SER ILE LEU MET LEU PRO SEQRES 3 B 84 GLU GLU VAL GLU GLU VAL ILE GLY ASN LYS PRO GLU SER SEQRES 4 B 84 ASP ILE LEU VAL HIS THR ALA TYR ASP GLU SER THR ASP SEQRES 5 B 84 GLU ASN VAL MET LEU LEU THR SER ASP ALA PRO GLU TYR SEQRES 6 B 84 LYS PRO TRP ALA LEU VAL ILE GLN ASP SER ASN GLY GLU SEQRES 7 B 84 ASN LYS ILE LYS MET LEU HET IMD A1500 5 HETNAM IMD IMIDAZOLE FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 HOH *71(H2 O) HELIX 1 1 SER A 5 THR A 12 1 8 HELIX 2 2 PRO A 26 ILE A 33 1 8 HELIX 3 3 LEU B 4 THR B 12 1 9 HELIX 4 4 GLU B 27 ILE B 33 1 7 SHEET 1 A 5 SER A 21 MET A 24 0 SHEET 2 A 5 ILE A 41 ASP A 48 -1 N VAL A 43 O ILE A 22 SHEET 3 A 5 GLU A 53 SER A 60 -1 N THR A 59 O LEU A 42 SHEET 4 A 5 PRO A 67 GLN A 73 -1 N GLN A 73 O ASN A 54 SHEET 5 A 5 ASN A 79 MET A 83 -1 N LYS A 82 O LEU A 70 SHEET 1 B 5 ILE B 22 MET B 24 0 SHEET 2 B 5 ILE B 41 ASP B 48 -1 N VAL B 43 O ILE B 22 SHEET 3 B 5 GLU B 53 SER B 60 -1 N THR B 59 O LEU B 42 SHEET 4 B 5 PRO B 67 GLN B 73 -1 N GLN B 73 O ASN B 54 SHEET 5 B 5 ASN B 79 MET B 83 -1 N LYS B 82 O LEU B 70 CISPEP 1 ALA A 62 PRO A 63 0 0.46 CISPEP 2 ALA B 62 PRO B 63 0 -0.23 SITE 1 AC1 7 GLN A 73 GLY A 77 ASN A 79 LEU B 23 SITE 2 AC1 7 LEU B 25 GLU B 28 GLU B 78 CRYST1 42.092 59.387 73.583 90.00 90.00 90.00 P 21 21 21 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 0.023757 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013590 0.00000 MTRIX1 1 -0.351630 0.019290 0.935940 14.17055 1 MTRIX2 1 -0.009420 -0.999810 0.017070 37.25146 1 MTRIX3 1 0.936090 -0.002820 0.351750 -9.82261 1