10 20 30 40 50 60 70 80 1R7L - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-OCT-03 1R7L
TITLE 2.0 A CRYSTAL STRUCTURE OF A PHAGE PROTEIN FROM BACILLUS TITLE 2 CEREUS ATCC 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 KEYWDS 2 SANDWICH, PSI, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER KEYWDS 3 FOR STRUCTURAL GENOMICS, MCSG, UNKNOWN FUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR R.ZHANG,G.JOACHIMIAK,F.COLLART,A.JOACHIMIAK,MIDWEST CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (MCSG)
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 JRNL TITL 2 CEREUS, A 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 1
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) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.83 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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-03. REMARK 100 THE RCSB ID CODE IS RCSB020535.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 REMARK 280 CA(OAC)2, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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