PDB Short entry for 1Y2G HEADER CELL CYCLE 22-NOV-04 1Y2G TITLE CRYSTAL STRUCTURE OF ZIPA IN COMPLEX WITH AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION PROTEIN ZIPA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ZIPA KEYWDS CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR L.MOSYAK,T.S.RUSH REVDAT 4 23-AUG-23 1Y2G 1 REMARK REVDAT 3 24-FEB-09 1Y2G 1 VERSN REVDAT 2 12-APR-05 1Y2G 1 JRNL REVDAT 1 01-MAR-05 1Y2G 0 JRNL AUTH T.S.RUSH,J.A.GRANT,L.MOSYAK,A.NICHOLLS JRNL TITL A SHAPE-BASED 3-D SCAFFOLD HOPPING METHOD AND ITS JRNL TITL 2 APPLICATION TO A BACTERIAL PROTEIN-PROTEIN INTERACTION JRNL REF J.MED.CHEM. V. 48 1489 2005 JRNL REFN ISSN 0022-2623 JRNL PMID 15743191 JRNL DOI 10.1021/JM040163O REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 606413.330 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 21488 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) : 0.207 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2996 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2171 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.60000 REMARK 3 B22 (A**2) : -2.51000 REMARK 3 B33 (A**2) : 8.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 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) : 1.740 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.730 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.800 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.240 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 48.23 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CL3.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CL3.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y2G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000031031. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1F46 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, MES, PH 6.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.76050 REMARK 290 SMTRY3 2 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 LYS A 5 REMARK 465 ASN A 143 REMARK 465 ALA A 144 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 PRO A 51 36.02 -73.08 REMARK 500 ASP A 76 -87.82 -38.54 REMARK 500 PHE A 77 156.82 -21.04 REMARK 500 SER A 90 -107.85 -133.90 REMARK 500 ASP A 118 -168.79 -79.96 REMARK 500 ASP B 41 135.47 -36.43 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 CL3 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y2F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZIPA IN COMPLEX WITH AN INHIBITOR DBREF 1Y2G A 5 144 UNP P77173 ZIPA_ECOLI 189 328 DBREF 1Y2G B 5 144 UNP P77173 ZIPA_ECOLI 189 328 SEQRES 1 A 140 LYS ARG LYS GLU ALA VAL ILE ILE MET ASN VAL ALA ALA SEQRES 2 A 140 HIS HIS GLY SER GLU LEU ASN GLY GLU LEU LEU LEU ASN SEQRES 3 A 140 SER ILE GLN GLN ALA GLY PHE ILE PHE GLY ASP MET ASN SEQRES 4 A 140 ILE TYR HIS ARG HIS LEU SER PRO ASP GLY SER GLY PRO SEQRES 5 A 140 ALA LEU PHE SER LEU ALA ASN MET VAL LYS PRO GLY THR SEQRES 6 A 140 PHE ASP PRO GLU MET LYS ASP PHE THR THR PRO GLY VAL SEQRES 7 A 140 THR ILE PHE MET GLN VAL PRO SER TYR GLY ASP GLU LEU SEQRES 8 A 140 GLN ASN PHE LYS LEU MET LEU GLN SER ALA GLN HIS ILE SEQRES 9 A 140 ALA ASP GLU VAL GLY GLY VAL VAL LEU ASP ASP GLN ARG SEQRES 10 A 140 ARG MET MET THR PRO GLN LYS LEU ARG GLU TYR GLN ASP SEQRES 11 A 140 ILE ILE ARG GLU VAL LYS ASP ALA ASN ALA SEQRES 1 B 140 LYS ARG LYS GLU ALA VAL ILE ILE MET ASN VAL ALA ALA SEQRES 2 B 140 HIS HIS GLY SER GLU LEU ASN GLY GLU LEU LEU LEU ASN SEQRES 3 B 140 SER ILE GLN GLN ALA GLY PHE ILE PHE GLY ASP MET ASN SEQRES 4 B 140 ILE TYR HIS ARG HIS LEU SER PRO ASP GLY SER GLY PRO SEQRES 5 B 140 ALA LEU PHE SER LEU ALA ASN MET VAL LYS PRO GLY THR SEQRES 6 B 140 PHE ASP PRO GLU MET LYS ASP PHE THR THR PRO GLY VAL SEQRES 7 B 140 THR ILE PHE MET GLN VAL PRO SER TYR GLY ASP GLU LEU SEQRES 8 B 140 GLN ASN PHE LYS LEU MET LEU GLN SER ALA GLN HIS ILE SEQRES 9 B 140 ALA ASP GLU VAL GLY GLY VAL VAL LEU ASP ASP GLN ARG SEQRES 10 B 140 ARG MET MET THR PRO GLN LYS LEU ARG GLU TYR GLN ASP SEQRES 11 B 140 ILE ILE ARG GLU VAL LYS ASP ALA ASN ALA HET CL3 A 301 26 HETNAM CL3 N-METHYL-N-[3-(6-PHENYL[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN- HETNAM 2 CL3 3-YL)PHENYL]ACETAMIDE FORMUL 3 CL3 C20 H17 N5 O FORMUL 4 HOH *223(H2 O) HELIX 1 1 GLY A 25 ALA A 35 1 11 HELIX 2 2 ASP A 41 ASN A 43 5 3 HELIX 3 3 ASP A 93 GLY A 113 1 21 HELIX 4 4 THR A 125 ALA A 142 1 18 HELIX 5 5 GLY B 25 ALA B 35 1 11 HELIX 6 6 ASP B 41 ASN B 43 5 3 HELIX 7 7 ASP B 93 GLY B 113 1 21 HELIX 8 8 THR B 125 ASN B 143 1 19 SHEET 1 A 6 ILE A 38 PHE A 39 0 SHEET 2 A 6 TYR A 45 HIS A 48 -1 O HIS A 46 N ILE A 38 SHEET 3 A 6 ALA A 57 ASN A 63 -1 O LEU A 58 N ARG A 47 SHEET 4 A 6 GLY A 81 VAL A 88 -1 O THR A 83 N ALA A 62 SHEET 5 A 6 ALA A 9 ALA A 16 -1 N ALA A 9 O VAL A 88 SHEET 6 A 6 VAL A 115 LEU A 117 -1 O LEU A 117 N ASN A 14 SHEET 1 B 2 LEU A 23 ASN A 24 0 SHEET 2 B 2 THR A 78 THR A 79 -1 O THR A 79 N LEU A 23 SHEET 1 C 6 ILE B 38 GLY B 40 0 SHEET 2 C 6 ILE B 44 HIS B 48 -1 O ILE B 44 N GLY B 40 SHEET 3 C 6 ALA B 57 ASN B 63 -1 O LEU B 58 N ARG B 47 SHEET 4 C 6 GLY B 81 VAL B 88 -1 O THR B 83 N ALA B 62 SHEET 5 C 6 ALA B 9 ALA B 16 -1 N ILE B 11 O MET B 86 SHEET 6 C 6 VAL B 115 LEU B 117 -1 O LEU B 117 N ASN B 14 SHEET 1 D 2 LEU B 23 ASN B 24 0 SHEET 2 D 2 THR B 78 THR B 79 -1 O THR B 79 N LEU B 23 CISPEP 1 LYS A 66 PRO A 67 0 0.40 CISPEP 2 VAL A 88 PRO A 89 0 -0.21 CISPEP 3 LYS B 66 PRO B 67 0 -0.45 CISPEP 4 VAL B 88 PRO B 89 0 1.04 SITE 1 AC1 7 ILE A 12 MET A 42 ILE A 44 ALA A 62 SITE 2 AC1 7 PRO A 67 GLY A 68 PHE A 85 CRYST1 52.695 39.521 70.271 90.00 104.97 90.00 P 1 21 1 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 0.018977 0.000000 0.005074 0.00000 SCALE2 0.000000 0.025303 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014731 0.00000