HEADER HYDROLASE 04-MAR-06 2DFW OBSLTE 04-AUG-09 2DFW 3IF5 TITLE CRYSTAL STRUCTURE OF A MAJOR FRAGMENT OF THE SALT-TOLERANT TITLE 2 GLUTAMINASE FROM MICROCOCCUS LUTEUS K-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SALT-TOLERANT GLUTAMINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINALLY TRUNCATED FRAGMENT(RESIDUES 1-396); COMPND 5 EC: 3.5.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICROCOCCUS LUTEUS; SOURCE 3 ORGANISM_TAXID: 1270; SOURCE 4 STRAIN: K-3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKK223-3 KEYWDS ALPHA/BETA STRUCTURE, STRUCTURAL GENOMICS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.YOSHIMUNE,Y.SHIRAKIHARA,A.SHIRATORI,M.WAKAYAMA, AUTHOR 2 P.CHANTAWANNAKUL,M.MORIGUCHI REVDAT 3 04-AUG-09 2DFW 1 OBSLTE REVDAT 2 24-FEB-09 2DFW 1 VERSN REVDAT 1 18-JUL-06 2DFW 0 JRNL AUTH K.YOSHIMUNE,Y.SHIRAKIHARA,A.SHIRATORI,M.WAKAYAMA, JRNL AUTH 2 P.CHANTAWANNAKUL,M.MORIGUCHI JRNL TITL CRYSTAL STRUCTURE OF A MAJOR FRAGMENT OF THE JRNL TITL 2 SALT-TOLERANT GLUTAMINASE FROM MICROCOCCUS LUTEUS JRNL TITL 3 K-3 JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 346 1118 2006 JRNL REFN ISSN 0006-291X JRNL PMID 16793004 JRNL DOI 10.1016/J.BBRC.2006.04.188 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.44 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) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 6887488.900 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 32656 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) : 0.215 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1645 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) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 36.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2126 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 118 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2898 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.03000 REMARK 3 B22 (A**2) : 9.24000 REMARK 3 B33 (A**2) : -14.28000 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.06 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 : 0.37 REMARK 3 BSOL : 65.62 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.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FILE CONTAINS FRIEDEL PAIRS. REMARK 4 REMARK 4 2DFW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-06. REMARK 100 THE RCSB ID CODE IS RCSB025369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9793, 0.9700 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE- REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14800 REMARK 200 R SYM FOR SHELL (I) : 0.10700 REMARK 200 FOR SHELL : 11.900 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: THE FILE CONTAINS FRIEDEL PAIRS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION CONSISTING OF REMARK 280 0.1M HEPES, 0.84M SODIUM CITRATE, PROTEIN SOLUTION CONSISTING REMARK 280 OF 5MG/ML PROTEIN, 0.05M HEPES, 0.7M SODIUM CITRATE, 5MM REMARK 280 MGCL2, 5% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 58.20000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.45000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.20000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.45000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.20000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.45000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.20000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.45000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 72.45000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 72.45000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 72.45000 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 72.45000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 58.20000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 58.20000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 58.20000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 57.85000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 58.20000 REMARK 290 SMTRY3 16 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 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 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 -1.000000 0.000000 0.000000 57.85000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 58.20000 REMARK 350 BIOMT3 2 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 GLY A 353 REMARK 465 ALA A 354 REMARK 465 GLU A 355 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 322 NZ LYS A 356 1.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CH2 TRP A 369 O HOH A 426 14555 1.71 REMARK 500 NH2 ARG A 303 CZ2 TRP A 369 14555 1.83 REMARK 500 CZ3 TRP A 369 O HOH A 426 14555 1.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 377 CA ALA A 377 CB -0.157 REMARK 500 ALA A 396 CA ALA A 396 CB 0.188 REMARK 500 ALA A 396 C ALA A 396 OXT 0.139 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 367 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 PRO A 367 N - CA - C ANGL. DEV. = -26.7 DEGREES REMARK 500 ARG A 368 N - CA - C ANGL. DEV. = -26.5 DEGREES REMARK 500 ALA A 377 CB - CA - C ANGL. DEV. = -10.9 DEGREES REMARK 500 ALA A 378 N - CA - C ANGL. DEV. = -25.1 DEGREES REMARK 500 ALA A 396 C - N - CA ANGL. DEV. = 15.6 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 GLN A 63 -142.01 51.18 REMARK 500 SER A 64 -19.91 -48.32 REMARK 500 HIS A 106 42.35 35.81 REMARK 500 LEU A 124 -80.18 -28.56 REMARK 500 PRO A 270 125.60 -37.00 REMARK 500 SER A 279 104.31 -174.99 REMARK 500 ASP A 325 -83.65 -78.56 REMARK 500 ARG A 336 -160.39 -116.99 REMARK 500 ARG A 351 -72.07 -69.13 REMARK 500 TYR A 366 -12.23 -140.74 REMARK 500 TRP A 369 146.86 -175.01 REMARK 500 GLN A 370 -53.71 -22.21 REMARK 500 ALA A 377 26.24 -74.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 124 24.3 L L OUTSIDE RANGE REMARK 500 PRO A 367 50.5 L L OUTSIDE RANGE REMARK 500 ARG A 368 50.0 L L OUTSIDE RANGE REMARK 500 ALA A 378 52.6 L L OUTSIDE RANGE 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 A 457 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH A 549 DISTANCE = 5.56 ANGSTROMS REMARK 525 HOH A 580 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH A 593 DISTANCE = 5.08 ANGSTROMS REMARK 525 HOH A 628 DISTANCE = 6.00 ANGSTROMS DBREF 2DFW A 1 396 UNP Q4U1A6 Q4U1A6_MICLU 1 396 SEQRES 1 A 396 MET ARG HIS PRO ILE PRO ASP TYR LEU ALA SER LEU VAL SEQRES 2 A 396 THR GLU LEU GLY ALA VAL ASN PRO GLY GLU THR ALA GLN SEQRES 3 A 396 TYR ILE PRO VAL LEU ALA GLU ALA ASP PRO ASP ARG PHE SEQRES 4 A 396 GLY ILE ALA LEU ALA THR PRO THR GLY ARG LEU HIS CYS SEQRES 5 A 396 ALA GLY ASP ALA ASP VAL GLU PHE THR ILE GLN SER ALA SEQRES 6 A 396 SER LYS PRO PHE THR TYR ALA ALA ALA LEU VAL ASP ARG SEQRES 7 A 396 GLY PHE ALA ALA VAL ASP ARG GLN VAL GLY LEU ASN PRO SEQRES 8 A 396 SER GLY GLU ALA PHE ASN GLU LEU SER LEU GLU ALA GLU SEQRES 9 A 396 SER HIS ARG PRO ASP ASN ALA MSE ILE ASN ALA GLY ALA SEQRES 10 A 396 LEU ALA VAL HIS GLN LEU LEU VAL GLY PRO GLU ALA SER SEQRES 11 A 396 ARG LYS GLU ARG LEU ASP ARG ALA VAL GLU ILE MSE SER SEQRES 12 A 396 LEU LEU ALA GLY ARG ARG LEU SER VAL ASP TRP GLU THR SEQRES 13 A 396 TYR GLU SER GLU MSE ALA VAL SER ASP ARG ASN LEU SER SEQRES 14 A 396 LEU ALA HIS MSE LEU ARG SER TYR GLY VAL LEU GLN ASP SEQRES 15 A 396 SER ALA GLU GLU ILE VAL ALA GLY TYR VAL ALA GLN CYS SEQRES 16 A 396 ALA VAL LEU VAL THR VAL LYS ASP LEU ALA VAL MSE GLY SEQRES 17 A 396 ALA CYS LEU ALA THR GLY GLY ILE HIS PRO MET THR GLY SEQRES 18 A 396 GLU ARG MET LEU PRO SER ILE VAL ALA ARG ARG VAL VAL SEQRES 19 A 396 SER VAL MSE THR SER SER GLY MSE TYR ASP ALA ALA GLY SEQRES 20 A 396 GLN TRP LEU ALA ASP VAL GLY ILE PRO ALA LYS SER GLY SEQRES 21 A 396 VAL ALA GLY GLY VAL LEU GLY ALA LEU PRO GLY ARG VAL SEQRES 22 A 396 GLY ILE GLY VAL PHE SER PRO ARG LEU ASP GLU VAL GLY SEQRES 23 A 396 ASN SER ALA ARG GLY VAL LEU ALA CYS ARG ARG LEU SER SEQRES 24 A 396 GLU ASP PHE ARG LEU HIS LEU MSE ASP GLY ASP SER LEU SEQRES 25 A 396 GLY GLY THR ALA VAL ARG PHE VAL GLU ARG GLU GLY ASP SEQRES 26 A 396 ARG VAL PHE LEU HIS LEU GLN GLY VAL ILE ARG PHE GLY SEQRES 27 A 396 GLY ALA GLU ALA VAL LEU ASP ALA LEU THR ASP LEU ARG SEQRES 28 A 396 THR GLY ALA GLU LYS PRO GLY THR GLY TRP ASP ALA ALA SEQRES 29 A 396 VAL TYR PRO ARG TRP GLN GLU ALA ALA ALA ASP ARG ALA SEQRES 30 A 396 ALA LEU SER ALA ALA THR GLY GLY GLY ALA VAL HIS GLU SEQRES 31 A 396 ALA ALA ALA ALA ALA ALA MODRES 2DFW MSE A 112 MET SELENOMETHIONINE MODRES 2DFW MSE A 142 MET SELENOMETHIONINE MODRES 2DFW MSE A 161 MET SELENOMETHIONINE MODRES 2DFW MSE A 173 MET SELENOMETHIONINE MODRES 2DFW MSE A 207 MET SELENOMETHIONINE MODRES 2DFW MSE A 237 MET SELENOMETHIONINE MODRES 2DFW MSE A 242 MET SELENOMETHIONINE MODRES 2DFW MSE A 307 MET SELENOMETHIONINE HET MSE A 112 8 HET MSE A 142 8 HET MSE A 161 8 HET MSE A 173 8 HET MSE A 207 8 HET MSE A 237 8 HET MSE A 242 8 HET MSE A 307 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 HOH *234(H2 O) HELIX 1 1 PRO A 4 GLY A 17 1 14 HELIX 2 2 ILE A 28 GLU A 33 1 6 HELIX 3 3 GLN A 63 ALA A 65 5 3 HELIX 4 4 SER A 66 GLY A 79 1 14 HELIX 5 5 GLY A 79 ARG A 85 1 7 HELIX 6 6 GLU A 98 ALA A 103 1 6 HELIX 7 7 ILE A 113 LEU A 124 1 12 HELIX 8 8 SER A 130 GLY A 147 1 18 HELIX 9 9 ASP A 153 ALA A 162 1 10 HELIX 10 10 SER A 164 TYR A 177 1 14 HELIX 11 11 SER A 183 ALA A 196 1 14 HELIX 12 12 THR A 200 THR A 213 1 14 HELIX 13 13 PRO A 226 GLY A 241 1 16 HELIX 14 14 ALA A 245 VAL A 253 1 9 HELIX 15 15 SER A 288 ARG A 303 1 16 HELIX 16 16 LEU A 312 THR A 315 5 4 HELIX 17 17 ARG A 336 LEU A 350 1 15 HELIX 18 18 TRP A 369 ALA A 377 1 9 HELIX 19 19 LEU A 379 GLY A 384 1 6 SHEET 1 A 5 LEU A 50 GLY A 54 0 SHEET 2 A 5 GLY A 40 ALA A 44 -1 N LEU A 43 O HIS A 51 SHEET 3 A 5 VAL A 273 PHE A 278 -1 O PHE A 278 N GLY A 40 SHEET 4 A 5 GLY A 264 LEU A 269 -1 N LEU A 269 O VAL A 273 SHEET 5 A 5 ALA A 257 SER A 259 -1 N LYS A 258 O LEU A 266 SHEET 1 B 2 PHE A 60 THR A 61 0 SHEET 2 B 2 LEU A 198 VAL A 199 -1 O VAL A 199 N PHE A 60 SHEET 1 C 4 VAL A 317 GLU A 323 0 SHEET 2 C 4 ARG A 326 GLY A 333 -1 O PHE A 328 N GLU A 321 SHEET 3 C 4 GLY A 358 VAL A 365 1 O GLY A 360 N VAL A 327 SHEET 4 C 4 VAL A 388 ALA A 391 1 O GLU A 390 N THR A 359 LINK C ALA A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N ILE A 113 1555 1555 1.33 LINK C ILE A 141 N MSE A 142 1555 1555 1.33 LINK C MSE A 142 N SER A 143 1555 1555 1.33 LINK C GLU A 160 N MSE A 161 1555 1555 1.33 LINK C MSE A 161 N ALA A 162 1555 1555 1.33 LINK C HIS A 172 N MSE A 173 1555 1555 1.33 LINK C MSE A 173 N LEU A 174 1555 1555 1.33 LINK C VAL A 206 N MSE A 207 1555 1555 1.33 LINK C MSE A 207 N GLY A 208 1555 1555 1.33 LINK C VAL A 236 N MSE A 237 1555 1555 1.34 LINK C MSE A 237 N THR A 238 1555 1555 1.33 LINK C GLY A 241 N MSE A 242 1555 1555 1.32 LINK C MSE A 242 N TYR A 243 1555 1555 1.33 LINK C LEU A 306 N MSE A 307 1555 1555 1.33 LINK C MSE A 307 N ASP A 308 1555 1555 1.33 CRYST1 115.700 116.400 144.900 90.00 90.00 90.00 F 2 2 2 16 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 0.008643 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006901 0.00000