HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-OCT-03 1R7L TITLE 2.0 A CRYSTAL STRUCTURE OF A PHAGE PROTEIN FROM BACILLUS CEREUS ATCC TITLE 2 14579 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 ATCC: 14579; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDM68 KEYWDS STRUCTURAL GENOMICS, PHAGE PROTEIN, TWO LAYERS ALPHA-BETA SANDWICH, KEYWDS 2 PSI, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, MCSG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,G.JOACHIMIAK,F.COLLART,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 5 14-FEB-24 1R7L 1 SEQADV REVDAT 4 24-FEB-09 1R7L 1 VERSN REVDAT 3 04-JUL-06 1R7L 1 JRNL REVDAT 2 18-JAN-05 1R7L 1 AUTHOR KEYWDS REMARK REVDAT 1 06-JUL-04 1R7L 0 JRNL AUTH R.ZHANG,G.JOACHIMIAK,S.JIANG,A.CIPRIANI,F.COLLART, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL STRUCTURE OF PHAGE PROTEIN BC1872 FROM BACILLUS CEREUS, A JRNL TITL 2 SINGLETON WITH NEW FOLD JRNL REF PROTEINS V. 64 280 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 16596646 JRNL DOI 10.1002/PROT.20910 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 444377.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 32415 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) : 0.223 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1628 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4497 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 256 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1690 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.14000 REMARK 3 B22 (A**2) : -3.42000 REMARK 3 B33 (A**2) : -4.72000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.27000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 60.02 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FREIDEL PAIRS WERE USED IN THE REMARK 3 REFINEMENT. REMARK 4 REMARK 4 1R7L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795, 0.9798, 0.9465 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SBCCOLLECT REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17557 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 8.120 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.51800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.1M MES, 0.2M CA(OAC)2, REMARK 280 PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 33.16900 REMARK 290 SMTRY3 2 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 300 REMARK: MOLECULE A AND MOLECULE B REPRESENT THE DIMER IN THE REMARK 300 ASYMMETRIC UNIT. 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 ASN A -7 REMARK 465 ASP A 97 REMARK 465 ILE A 98 REMARK 465 GLU A 99 REMARK 465 LEU A 100 REMARK 465 GLN A 101 REMARK 465 ASP A 102 REMARK 465 ASP B 102 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 ALA A 0 118.22 -161.36 REMARK 500 ARG A 29 -20.68 -148.99 REMARK 500 VAL B 76 141.08 -39.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC22846 RELATED DB: TARGETDB DBREF 1R7L A 1 102 UNP Q81EU2 Q81EU2_BACCR 1 102 DBREF 1R7L B 1 102 UNP Q81EU2 Q81EU2_BACCR 1 102 SEQADV 1R7L ASN A -7 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L LEU A -6 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L TYR A -5 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L PHE A -4 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L GLN A -3 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L SER A -2 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L ASN A -1 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L ALA A 0 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L ASN B -7 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L LEU B -6 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L TYR B -5 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L PHE B -4 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L GLN B -3 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L SER B -2 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L ASN B -1 UNP Q81EU2 EXPRESSION TAG SEQADV 1R7L ALA B 0 UNP Q81EU2 EXPRESSION TAG SEQRES 1 A 110 ASN LEU TYR PHE GLN SER ASN ALA MET LYS PRO ARG ASP SEQRES 2 A 110 ILE ASN LYS LEU ILE ALA SER LYS ILE PHE GLY TYR GLU SEQRES 3 A 110 ILE LYS ASP ASP ASN ILE ILE LYS ASP GLY ARG TYR ARG SEQRES 4 A 110 LEU GLY ILE PRO LEU TYR SER GLN ASN ILE GLU SER ALA SEQRES 5 A 110 TRP GLN VAL VAL GLU LYS LEU GLU TYR ASP VAL LYS VAL SEQRES 6 A 110 THR LYS THR ASP LEU LYS PRO LYS TYR GLN VAL HIS VAL SEQRES 7 A 110 PHE VAL PRO GLY GLY VAL LYS MET VAL PHE ALA GLU THR SEQRES 8 A 110 ALA PRO MET ALA ILE CYS LYS GLY ALA LEU ALA SER VAL SEQRES 9 A 110 ASP ILE GLU LEU GLN ASP SEQRES 1 B 110 ASN LEU TYR PHE GLN SER ASN ALA MET LYS PRO ARG ASP SEQRES 2 B 110 ILE ASN LYS LEU ILE ALA SER LYS ILE PHE GLY TYR GLU SEQRES 3 B 110 ILE LYS ASP ASP ASN ILE ILE LYS ASP GLY ARG TYR ARG SEQRES 4 B 110 LEU GLY ILE PRO LEU TYR SER GLN ASN ILE GLU SER ALA SEQRES 5 B 110 TRP GLN VAL VAL GLU LYS LEU GLU TYR ASP VAL LYS VAL SEQRES 6 B 110 THR LYS THR ASP LEU LYS PRO LYS TYR GLN VAL HIS VAL SEQRES 7 B 110 PHE VAL PRO GLY GLY VAL LYS MET VAL PHE ALA GLU THR SEQRES 8 B 110 ALA PRO MET ALA ILE CYS LYS GLY ALA LEU ALA SER VAL SEQRES 9 B 110 ASP ILE GLU LEU GLN ASP FORMUL 3 HOH *102(H2 O) HELIX 1 1 LYS A 2 ILE A 14 1 13 HELIX 2 2 ASP A 27 ARG A 29 5 3 HELIX 3 3 ASN A 40 LEU A 51 1 12 HELIX 4 4 THR A 83 SER A 95 1 13 HELIX 5 5 LYS B 2 ILE B 14 1 13 HELIX 6 6 ASP B 27 ARG B 29 5 3 HELIX 7 7 ASN B 40 LEU B 51 1 12 HELIX 8 8 THR B 83 SER B 95 1 13 SHEET 1 A 3 ILE A 19 LYS A 20 0 SHEET 2 A 3 ASN A 23 LYS A 26 -1 O ASN A 23 N LYS A 20 SHEET 3 A 3 TYR A 30 LEU A 32 -1 O TYR A 30 N LYS A 26 SHEET 1 B 6 LYS A 77 ALA A 81 0 SHEET 2 B 6 TYR A 66 PHE A 71 -1 N VAL A 70 O LYS A 77 SHEET 3 B 6 ASP A 54 LYS A 59 -1 N LYS A 56 O HIS A 69 SHEET 4 B 6 ASP B 54 LYS B 59 -1 O VAL B 55 N LYS A 59 SHEET 5 B 6 TYR B 66 PHE B 71 -1 O GLN B 67 N THR B 58 SHEET 6 B 6 LYS B 77 ALA B 81 -1 O LYS B 77 N VAL B 70 SHEET 1 C 2 ASN B 23 LYS B 26 0 SHEET 2 C 2 TYR B 30 GLY B 33 -1 O TYR B 30 N LYS B 26 CISPEP 1 LYS A 63 PRO A 64 0 -0.18 CISPEP 2 LYS B 63 PRO B 64 0 -0.28 CRYST1 37.002 66.338 53.966 90.00 95.29 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 0.027026 0.000000 0.002502 0.00000 SCALE2 0.000000 0.015074 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018609 0.00000