HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 16-AUG-06 2I2L TITLE X-RAY CRYSTAL STRUCTURE OF PROTEIN YOPX FROM BACILLUS TITLE 2 SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 3 SR411. COMPND MOL_ID: 1; COMPND 2 MOLECULE: YOPX PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YOPX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS NESG, SR411, YOPX, O34401, STRUCTURAL GENOMICS, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.M.VOROBIEV,W.ZHOU,J.SEETHARAMAN,F.FOROUHAR,A.A.KUZIN, AUTHOR 2 C.K.HO,H.JANJUA,K.CUNNINGHAM,L.C.MA,R.XIAO,J.LIU,T.ACTON, AUTHOR 3 G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL AUTHOR 4 GENOMICS CONSORTIUM (NESG) REVDAT 2 24-FEB-09 2I2L 1 VERSN REVDAT 1 29-AUG-06 2I2L 0 JRNL AUTH S.M.VOROBIEV,W.ZHOU,J.SEETHARAMAN,F.FOROUHAR, JRNL AUTH 2 A.A.KUZIN,C.K.HO,K.CUNNINGHAM,L.C.MA,R.XIAO,J.LIU, JRNL AUTH 3 T.ACTON,G.T.MONTELIONE,J.F.HUNT,L.TONG JRNL TITL CRYSTAL STRUCTURE OF THE HYPOTHETICAL PROTEIN YOPX JRNL TITL 2 FROM BACILLUS SUBTILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 214814.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.3 REMARK 3 NUMBER OF REFLECTIONS : 19848 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) : 0.241 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 790 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2398 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.048 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2968 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.97000 REMARK 3 B22 (A**2) : -5.97000 REMARK 3 B33 (A**2) : 11.94000 REMARK 3 B12 (A**2) : 1.13000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.41 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) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.97 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 : 0.26 REMARK 3 BSOL : 28.32 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 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FRIEDEL PAIRS WERE USED FOR REMARK 3 PHASING REMARK 4 REMARK 4 2I2L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB039057. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911, 0.97944, 0.96798 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23973 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.55700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD, SHELXE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.2M SODIUM ACETATE, REMARK 280 0.2M SODIUM THIOCYANATE, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.28667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.14333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.14333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 58.28667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 87.43000 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 ILE A 100 REMARK 465 SER A 101 REMARK 465 ALA A 102 REMARK 465 ASP A 103 REMARK 465 LEU A 135 REMARK 465 GLU A 136 REMARK 465 HIS A 137 REMARK 465 HIS A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 ILE B 100 REMARK 465 SER B 101 REMARK 465 ALA B 102 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS B 139 REMARK 465 HIS B 140 REMARK 465 HIS B 141 REMARK 465 HIS B 142 REMARK 465 ILE C 100 REMARK 465 SER C 101 REMARK 465 ALA C 102 REMARK 465 GLY C 132 REMARK 465 VAL C 133 REMARK 465 LYS C 134 REMARK 465 LEU C 135 REMARK 465 GLU C 136 REMARK 465 HIS C 137 REMARK 465 HIS C 138 REMARK 465 HIS C 139 REMARK 465 HIS C 140 REMARK 465 HIS C 141 REMARK 465 HIS C 142 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 THR A 38 OG1 CG2 REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 ILE A 73 CG1 CG2 CD1 REMARK 470 THR A 74 OG1 CG2 REMARK 470 ASP A 76 CG OD1 OD2 REMARK 470 ASP A 77 CG OD1 OD2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 SER A 80 OG REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 VAL A 112 CG1 CG2 REMARK 470 GLU A 113 CG CD OE1 OE2 REMARK 470 TYR A 114 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 123 CG1 CG2 REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 MSE B 1 CG SE CE REMARK 470 GLU B 19 CG CD OE1 OE2 REMARK 470 ARG B 50 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 ILE B 73 CG1 CG2 CD1 REMARK 470 THR B 74 OG1 CG2 REMARK 470 SER B 75 OG REMARK 470 ASP B 76 CG OD1 OD2 REMARK 470 ASP B 77 CG OD1 OD2 REMARK 470 LYS B 78 CG CD CE NZ REMARK 470 GLU B 79 CG CD OE1 OE2 REMARK 470 SER B 80 OG REMARK 470 SER B 81 OG REMARK 470 SER B 98 OG REMARK 470 LYS B 99 CG CD CE NZ REMARK 470 VAL B 112 CG1 CG2 REMARK 470 GLU B 113 CG CD OE1 OE2 REMARK 470 TYR B 114 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL B 123 CG1 CG2 REMARK 470 GLU B 128 CG CD OE1 OE2 REMARK 470 VAL B 133 CG1 CG2 REMARK 470 LYS B 134 CG CD CE NZ REMARK 470 GLU B 136 CG CD OE1 OE2 REMARK 470 GLU C 19 CG CD OE1 OE2 REMARK 470 ARG C 35 CG CD NE CZ NH1 NH2 REMARK 470 TYR C 37 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR C 38 OG1 CG2 REMARK 470 VAL C 42 CG1 CG2 REMARK 470 GLU C 79 CG CD OE1 OE2 REMARK 470 SER C 81 OG REMARK 470 ASP C 103 CG OD1 OD2 REMARK 470 VAL C 109 CG1 CG2 REMARK 470 GLU C 113 CG CD OE1 OE2 REMARK 470 GLU C 131 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY B 132 N - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 LEU B 135 CA - CB - CG ANGL. DEV. = 32.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 37 -75.91 -79.86 REMARK 500 THR A 38 -96.31 -100.99 REMARK 500 ARG A 50 -5.39 -54.55 REMARK 500 ARG A 61 31.08 73.37 REMARK 500 TYR A 66 -63.87 -137.51 REMARK 500 ASP A 67 38.40 -166.93 REMARK 500 ASP A 76 -90.69 -57.05 REMARK 500 ASP A 77 -74.37 -128.41 REMARK 500 LYS A 78 10.95 -159.00 REMARK 500 GLU A 113 -78.42 -78.95 REMARK 500 TYR A 114 38.30 -87.16 REMARK 500 ASN A 126 49.48 -142.72 REMARK 500 LEU A 130 48.60 -76.58 REMARK 500 THR B 3 -18.87 -150.25 REMARK 500 TYR B 37 -85.35 -82.83 REMARK 500 THR B 38 -82.86 -88.86 REMARK 500 ASP B 39 29.68 -141.28 REMARK 500 ASN B 49 99.88 -65.73 REMARK 500 TYR B 66 -138.36 -102.27 REMARK 500 ASP B 67 58.30 -108.25 REMARK 500 ASP B 76 -133.99 -88.20 REMARK 500 LYS B 78 23.49 -70.98 REMARK 500 GLU B 79 33.86 -83.19 REMARK 500 SER B 80 107.51 -175.62 REMARK 500 ASP B 82 142.39 179.29 REMARK 500 THR C 3 -2.26 -140.57 REMARK 500 TRP C 16 -27.52 -37.07 REMARK 500 TYR C 37 -90.59 -91.99 REMARK 500 ASP C 39 29.08 -163.76 REMARK 500 VAL C 45 165.47 175.06 REMARK 500 SER C 47 -18.93 -42.00 REMARK 500 ASP C 82 154.28 177.89 REMARK 500 ASN C 126 72.21 -154.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 124 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 214 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH C 225 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 268 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH C 236 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH A 269 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH B 248 DISTANCE = 7.82 ANGSTROMS REMARK 525 HOH B 251 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 275 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B 267 DISTANCE = 5.78 ANGSTROMS REMARK 525 HOH A 291 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH B 288 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH C 266 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH A 317 DISTANCE = 5.72 ANGSTROMS REMARK 525 HOH C 322 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH B 326 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH C 332 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH B 330 DISTANCE = 5.61 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SR411 RELATED DB: TARGETDB DBREF 2I2L A 1 134 UNP O34401 O34401_BACSU 1 134 DBREF 2I2L B 1 134 UNP O34401 O34401_BACSU 1 134 DBREF 2I2L C 1 134 UNP O34401 O34401_BACSU 1 134 SEQADV 2I2L MSE A 1 UNP O34401 MET 1 MODIFIED RESIDUE SEQADV 2I2L MSE A 13 UNP O34401 MET 13 MODIFIED RESIDUE SEQADV 2I2L MSE A 55 UNP O34401 MET 55 MODIFIED RESIDUE SEQADV 2I2L LEU A 135 UNP O34401 CLONING ARTIFACT SEQADV 2I2L GLU A 136 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS A 137 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS A 138 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS A 139 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS A 140 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS A 141 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS A 142 UNP O34401 CLONING ARTIFACT SEQADV 2I2L MSE B 1 UNP O34401 MET 1 MODIFIED RESIDUE SEQADV 2I2L MSE B 13 UNP O34401 MET 13 MODIFIED RESIDUE SEQADV 2I2L MSE B 55 UNP O34401 MET 55 MODIFIED RESIDUE SEQADV 2I2L LEU B 135 UNP O34401 CLONING ARTIFACT SEQADV 2I2L GLU B 136 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS B 137 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS B 138 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS B 139 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS B 140 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS B 141 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS B 142 UNP O34401 CLONING ARTIFACT SEQADV 2I2L MSE C 1 UNP O34401 MET 1 MODIFIED RESIDUE SEQADV 2I2L MSE C 13 UNP O34401 MET 13 MODIFIED RESIDUE SEQADV 2I2L MSE C 55 UNP O34401 MET 55 MODIFIED RESIDUE SEQADV 2I2L LEU C 135 UNP O34401 CLONING ARTIFACT SEQADV 2I2L GLU C 136 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS C 137 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS C 138 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS C 139 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS C 140 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS C 141 UNP O34401 CLONING ARTIFACT SEQADV 2I2L HIS C 142 UNP O34401 CLONING ARTIFACT SEQRES 1 A 142 MSE ASN THR ALA TYR ARG VAL TRP ASP GLY GLU GLN MSE SEQRES 2 A 142 HIS TYR TRP ASP ASP GLU GLY LEU SER LEU ILE ILE LYS SEQRES 3 A 142 SER ASN GLY ASP TRP THR LEU LYS ARG LEU TYR THR ASP SEQRES 4 A 142 VAL LEU VAL PRO VAL VAL ASP SER THR ASN ARG ASN ALA SEQRES 5 A 142 ALA LEU MSE TRP GLY ALA LYS VAL ARG GLY LYS PHE ILE SEQRES 6 A 142 TYR ASP ARG SER ILE VAL LYS ILE THR SER ASP ASP LYS SEQRES 7 A 142 GLU SER SER ASP VAL CYS GLU VAL LYS PHE SER ASP GLY SEQRES 8 A 142 VAL PHE GLN VAL ASP VAL SER LYS ILE SER ALA ASP TYR SEQRES 9 A 142 ASP VAL THR ALA VAL GLY TRP VAL GLU TYR ALA THR ILE SEQRES 10 A 142 GLU VAL ILE GLY ASP VAL TYR GLN ASN PRO GLU LEU LEU SEQRES 11 A 142 GLU GLY VAL LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 142 MSE ASN THR ALA TYR ARG VAL TRP ASP GLY GLU GLN MSE SEQRES 2 B 142 HIS TYR TRP ASP ASP GLU GLY LEU SER LEU ILE ILE LYS SEQRES 3 B 142 SER ASN GLY ASP TRP THR LEU LYS ARG LEU TYR THR ASP SEQRES 4 B 142 VAL LEU VAL PRO VAL VAL ASP SER THR ASN ARG ASN ALA SEQRES 5 B 142 ALA LEU MSE TRP GLY ALA LYS VAL ARG GLY LYS PHE ILE SEQRES 6 B 142 TYR ASP ARG SER ILE VAL LYS ILE THR SER ASP ASP LYS SEQRES 7 B 142 GLU SER SER ASP VAL CYS GLU VAL LYS PHE SER ASP GLY SEQRES 8 B 142 VAL PHE GLN VAL ASP VAL SER LYS ILE SER ALA ASP TYR SEQRES 9 B 142 ASP VAL THR ALA VAL GLY TRP VAL GLU TYR ALA THR ILE SEQRES 10 B 142 GLU VAL ILE GLY ASP VAL TYR GLN ASN PRO GLU LEU LEU SEQRES 11 B 142 GLU GLY VAL LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 142 MSE ASN THR ALA TYR ARG VAL TRP ASP GLY GLU GLN MSE SEQRES 2 C 142 HIS TYR TRP ASP ASP GLU GLY LEU SER LEU ILE ILE LYS SEQRES 3 C 142 SER ASN GLY ASP TRP THR LEU LYS ARG LEU TYR THR ASP SEQRES 4 C 142 VAL LEU VAL PRO VAL VAL ASP SER THR ASN ARG ASN ALA SEQRES 5 C 142 ALA LEU MSE TRP GLY ALA LYS VAL ARG GLY LYS PHE ILE SEQRES 6 C 142 TYR ASP ARG SER ILE VAL LYS ILE THR SER ASP ASP LYS SEQRES 7 C 142 GLU SER SER ASP VAL CYS GLU VAL LYS PHE SER ASP GLY SEQRES 8 C 142 VAL PHE GLN VAL ASP VAL SER LYS ILE SER ALA ASP TYR SEQRES 9 C 142 ASP VAL THR ALA VAL GLY TRP VAL GLU TYR ALA THR ILE SEQRES 10 C 142 GLU VAL ILE GLY ASP VAL TYR GLN ASN PRO GLU LEU LEU SEQRES 11 C 142 GLU GLY VAL LYS LEU GLU HIS HIS HIS HIS HIS HIS MODRES 2I2L MSE A 1 MET SELENOMETHIONINE MODRES 2I2L MSE A 13 MET SELENOMETHIONINE MODRES 2I2L MSE A 55 MET SELENOMETHIONINE MODRES 2I2L MSE B 1 MET SELENOMETHIONINE MODRES 2I2L MSE B 13 MET SELENOMETHIONINE MODRES 2I2L MSE B 55 MET SELENOMETHIONINE MODRES 2I2L MSE C 1 MET SELENOMETHIONINE MODRES 2I2L MSE C 13 MET SELENOMETHIONINE MODRES 2I2L MSE C 55 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 13 8 HET MSE A 55 8 HET MSE B 1 5 HET MSE B 13 8 HET MSE B 55 8 HET MSE C 1 8 HET MSE C 13 8 HET MSE C 55 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 4 HOH *134(H2 O) HELIX 1 1 GLY A 110 VAL A 112 5 3 HELIX 2 2 GLY B 110 VAL B 112 5 3 SHEET 1 A 3 MSE A 13 TYR A 15 0 SHEET 2 A 3 TYR A 5 TRP A 8 -1 N VAL A 7 O HIS A 14 SHEET 3 A 3 ALA A 53 TRP A 56 -1 O MSE A 55 N ARG A 6 SHEET 1 B 6 LEU A 41 ASP A 46 0 SHEET 2 B 6 TRP A 31 LEU A 36 -1 N ARG A 35 O VAL A 42 SHEET 3 B 6 SER A 22 ILE A 25 -1 N SER A 22 O LYS A 34 SHEET 4 B 6 LEU B 21 ILE B 25 -1 O ILE B 25 N LEU A 23 SHEET 5 B 6 TRP B 31 LEU B 36 -1 O LYS B 34 N SER B 22 SHEET 6 B 6 LEU B 41 ASP B 46 -1 O VAL B 42 N ARG B 35 SHEET 1 C 2 ALA A 58 VAL A 60 0 SHEET 2 C 2 LYS A 63 ILE A 65 -1 O LYS A 63 N VAL A 60 SHEET 1 D 3 VAL A 83 GLU A 85 0 SHEET 2 D 3 ARG A 68 THR A 74 -1 N ILE A 70 O CYS A 84 SHEET 3 D 3 ALA A 115 ASP A 122 -1 O GLU A 118 N VAL A 71 SHEET 1 E 3 LYS A 87 SER A 89 0 SHEET 2 E 3 VAL A 92 ASP A 96 -1 O GLN A 94 N LYS A 87 SHEET 3 E 3 VAL A 106 ALA A 108 -1 O THR A 107 N VAL A 95 SHEET 1 F 3 MSE B 13 TYR B 15 0 SHEET 2 F 3 TYR B 5 TRP B 8 -1 N VAL B 7 O HIS B 14 SHEET 3 F 3 ALA B 53 TRP B 56 -1 O MSE B 55 N ARG B 6 SHEET 1 G 2 ALA B 58 VAL B 60 0 SHEET 2 G 2 LYS B 63 ILE B 65 -1 O LYS B 63 N VAL B 60 SHEET 1 H 3 SER B 81 GLU B 85 0 SHEET 2 H 3 ARG B 68 THR B 74 -1 N ILE B 70 O CYS B 84 SHEET 3 H 3 ALA B 115 THR B 116 -1 O THR B 116 N ILE B 73 SHEET 1 I 3 SER B 81 GLU B 85 0 SHEET 2 I 3 ARG B 68 THR B 74 -1 N ILE B 70 O CYS B 84 SHEET 3 I 3 VAL B 119 ASP B 122 -1 O GLY B 121 N SER B 69 SHEET 1 J 3 LYS B 87 SER B 89 0 SHEET 2 J 3 VAL B 92 ASP B 96 -1 O VAL B 92 N SER B 89 SHEET 3 J 3 VAL B 106 ALA B 108 -1 O THR B 107 N VAL B 95 SHEET 1 K 4 MSE C 13 TYR C 15 0 SHEET 2 K 4 TYR C 5 TRP C 8 -1 N VAL C 7 O HIS C 14 SHEET 3 K 4 ALA C 53 VAL C 60 -1 O MSE C 55 N ARG C 6 SHEET 4 K 4 LYS C 63 TYR C 66 -1 O LYS C 63 N VAL C 60 SHEET 1 L 3 LEU C 21 ILE C 25 0 SHEET 2 L 3 TRP C 31 LEU C 36 -1 O LYS C 34 N SER C 22 SHEET 3 L 3 LEU C 41 ASP C 46 -1 O VAL C 42 N ARG C 35 SHEET 1 M 5 VAL C 106 ALA C 108 0 SHEET 2 M 5 VAL C 92 ASP C 96 -1 N VAL C 95 O THR C 107 SHEET 3 M 5 SER C 81 SER C 89 -1 N LYS C 87 O GLN C 94 SHEET 4 M 5 SER C 69 SER C 75 -1 N VAL C 71 O CYS C 84 SHEET 5 M 5 ALA C 115 ASP C 122 -1 O THR C 116 N THR C 74 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 LINK C GLN A 12 N MSE A 13 1555 1555 1.33 LINK C MSE A 13 N HIS A 14 1555 1555 1.33 LINK C LEU A 54 N MSE A 55 1555 1555 1.33 LINK C MSE A 55 N TRP A 56 1555 1555 1.32 LINK C MSE B 1 N ASN B 2 1555 1555 1.33 LINK C GLN B 12 N MSE B 13 1555 1555 1.33 LINK C MSE B 13 N HIS B 14 1555 1555 1.33 LINK C LEU B 54 N MSE B 55 1555 1555 1.33 LINK C MSE B 55 N TRP B 56 1555 1555 1.33 LINK C MSE C 1 N ASN C 2 1555 1555 1.33 LINK C GLN C 12 N MSE C 13 1555 1555 1.33 LINK C MSE C 13 N HIS C 14 1555 1555 1.33 LINK C LEU C 54 N MSE C 55 1555 1555 1.33 LINK C MSE C 55 N TRP C 56 1555 1555 1.33 CRYST1 99.521 99.521 87.430 90.00 90.00 120.00 P 32 2 1 18 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 0.010048 0.005801 0.000000 0.00000 SCALE2 0.000000 0.011603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011438 0.00000 HETATM 1 N MSE A 1 17.304 92.621 54.463 1.00 75.42 N HETATM 2 CA MSE A 1 16.140 93.038 53.628 1.00 75.24 C HETATM 3 C MSE A 1 16.557 93.807 52.375 1.00 71.41 C HETATM 4 O MSE A 1 17.238 94.829 52.458 1.00 71.84 O HETATM 5 CB MSE A 1 15.193 93.912 54.445 1.00 80.31 C HETATM 6 CG MSE A 1 13.987 94.373 53.655 1.00 86.98 C HETATM 7 SE MSE A 1 13.272 96.038 54.307 1.00 98.15 SE HETATM 8 CE MSE A 1 14.245 97.255 53.155 1.00 94.39 C