HEADER LIGASE 27-APR-07 2YYA TITLE CRYSTAL STRUCTURE OF GAR SYNTHETASE FROM AQUIFEX AEOLICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORIBOSYLAMINE--GLYCINE LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GARS, GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, COMPND 5 PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE; COMPND 6 EC: 6.3.4.13; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, GAR SYNTHETASE, ATP BINDING, KEYWDS 2 PURINE NUCLEOTIDE BIOSYNTHETIC PATHWAY, LIGASE, STRUCTURAL GENOMICS, KEYWDS 3 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 4 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR S.BABA,M.KANAGAWA,S.KURAMITSU,S.YOKOYAMA,G.KAWAI,G.SAMPEI,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 25-OCT-23 2YYA 1 REMARK REVDAT 3 08-DEC-10 2YYA 1 JRNL REVDAT 2 24-FEB-09 2YYA 1 VERSN REVDAT 1 30-OCT-07 2YYA 0 JRNL AUTH G.SAMPEI,S.BABA,M.KANAGAWA,H.YANAI,T.ISHII,H.KAWAI,Y.FUKAI, JRNL AUTH 2 A.EBIHARA,N.NAKAGAWA,G.KAWAI JRNL TITL CRYSTAL STRUCTURES OF GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, JRNL TITL 2 PURD, FROM THERMOPHILIC EUBACTERIA JRNL REF J.BIOCHEM. V. 148 429 2010 JRNL REFN ISSN 0021-924X JRNL PMID 20716513 JRNL DOI 10.1093/JB/MVQ088 REMARK 2 REMARK 2 RESOLUTION. 2.40 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 105493.920 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 32301 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) : 0.225 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3209 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4237 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 493 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6464 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.26000 REMARK 3 B22 (A**2) : -12.92000 REMARK 3 B33 (A**2) : 27.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 14.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.37 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) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.037 REMARK 3 BOND ANGLES (DEGREES) : 3.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.990 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) : 5.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 8.340 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.320 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.620; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 41.17 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 : ION.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 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YYA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : FIXED EXIT SI 111 DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33971 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06900 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.27700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2YW2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.10M SUCCINIC ACID, 15%W/V REMARK 280 POLYETHYLENE GLYCOL 3350, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 22.57600 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 GLU A 424 REMARK 465 GLU B 424 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 ASP A 125 CG OD1 OD2 REMARK 470 PHE A 126 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 127 CG CD OE1 OE2 REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 GLU A 131 CG CD OE1 OE2 REMARK 470 TYR A 132 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 133 CG1 CG2 REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 VAL A 136 CG1 CG2 REMARK 470 VAL A 159 CG1 CG2 REMARK 470 GLU A 160 CG CD OE1 OE2 REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 ILE A 163 CG1 CG2 CD1 REMARK 470 GLU A 164 CG CD OE1 OE2 REMARK 470 THR A 165 OG1 CG2 REMARK 470 LEU A 166 CG CD1 CD2 REMARK 470 ASP A 167 CG OD1 OD2 REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 169 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 170 CG CD1 CD2 REMARK 470 ASN A 171 CG OD1 ND2 REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 ILE A 174 CG1 CG2 CD1 REMARK 470 THR B 124 OG1 CG2 REMARK 470 ASP B 125 CG OD1 OD2 REMARK 470 PHE B 126 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 127 CG CD OE1 OE2 REMARK 470 LYS B 128 CG CD CE NZ REMARK 470 LYS B 130 CG CD CE NZ REMARK 470 GLU B 131 CG CD OE1 OE2 REMARK 470 TYR B 132 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL B 133 CG1 CG2 REMARK 470 GLU B 134 CG CD OE1 OE2 REMARK 470 LYS B 135 CG CD CE NZ REMARK 470 VAL B 136 CG1 CG2 REMARK 470 GLU B 157 CG CD OE1 OE2 REMARK 470 THR B 158 OG1 CG2 REMARK 470 VAL B 159 CG1 CG2 REMARK 470 GLU B 160 CG CD OE1 OE2 REMARK 470 LYS B 161 CG CD CE NZ REMARK 470 ILE B 163 CG1 CG2 CD1 REMARK 470 GLU B 164 CG CD OE1 OE2 REMARK 470 THR B 165 OG1 CG2 REMARK 470 LEU B 166 CG CD1 CD2 REMARK 470 ASP B 167 CG OD1 OD2 REMARK 470 ARG B 168 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 169 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 170 CG CD1 CD2 REMARK 470 ASN B 171 CG OD1 ND2 REMARK 470 LYS B 172 CG CD CE NZ REMARK 470 LYS B 173 CG CD CE NZ REMARK 470 ILE B 174 CG1 CG2 CD1 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 LYS A 32 C - N - CA ANGL. DEV. = 20.3 DEGREES REMARK 500 ASP A 50 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 LYS A 84 CD - CE - NZ ANGL. DEV. = 18.3 DEGREES REMARK 500 LYS A 84 CA - C - N ANGL. DEV. = -13.6 DEGREES REMARK 500 LYS A 84 O - C - N ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 PHE A 105 C - N - CA ANGL. DEV. = 15.4 DEGREES REMARK 500 LYS A 107 CA - C - N ANGL. DEV. = 13.7 DEGREES REMARK 500 LYS A 107 O - C - N ANGL. DEV. = -15.4 DEGREES REMARK 500 ILE A 140 C - N - CA ANGL. DEV. = 16.6 DEGREES REMARK 500 GLU A 157 C - N - CA ANGL. DEV. = 15.0 DEGREES REMARK 500 ILE A 174 CA - C - N ANGL. DEV. = -17.5 DEGREES REMARK 500 ILE A 174 O - C - N ANGL. DEV. = 18.9 DEGREES REMARK 500 PHE A 175 C - N - CA ANGL. DEV. = -15.9 DEGREES REMARK 500 ILE A 196 CG1 - CB - CG2 ANGL. DEV. = -18.6 DEGREES REMARK 500 ILE A 237 CA - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 ILE A 237 O - C - N ANGL. DEV. = 10.4 DEGREES REMARK 500 ASN A 238 CA - C - O ANGL. DEV. = 16.3 DEGREES REMARK 500 ASN A 238 CA - C - N ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG A 246 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 287 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 287 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 299 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 LEU A 309 CA - CB - CG ANGL. DEV. = -16.1 DEGREES REMARK 500 LEU A 309 CB - CG - CD1 ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG A 324 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 334 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 GLU A 356 CA - C - N ANGL. DEV. = -17.0 DEGREES REMARK 500 GLU A 356 O - C - N ANGL. DEV. = 15.6 DEGREES REMARK 500 ASP A 357 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 357 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 PHE A 361 O - C - N ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 395 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 395 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 395 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 TYR A 397 CZ - CE2 - CD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 TYR A 410 CG - CD2 - CE2 ANGL. DEV. = -5.4 DEGREES REMARK 500 TYR A 410 CZ - CE2 - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 LEU A 422 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 MET B 1 CG - SD - CE ANGL. DEV. = -10.5 DEGREES REMARK 500 LYS B 26 CD - CE - NZ ANGL. DEV. = 18.1 DEGREES REMARK 500 ALA B 31 CA - C - N ANGL. DEV. = -18.1 DEGREES REMARK 500 ALA B 31 O - C - N ANGL. DEV. = 9.9 DEGREES REMARK 500 LYS B 32 CB - CA - C ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP B 50 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG B 85 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 85 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 PRO B 139 CA - C - N ANGL. DEV. = 20.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 75 ANGLE DEVIATIONS. 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 ALA A 31 75.88 -114.92 REMARK 500 LYS A 32 -57.33 150.96 REMARK 500 ASP A 50 63.04 -106.64 REMARK 500 GLU A 76 10.83 -64.45 REMARK 500 ALA A 97 -6.13 -53.26 REMARK 500 LYS A 112 -0.65 -43.03 REMARK 500 TYR A 113 2.03 -152.18 REMARK 500 LYS A 130 -60.72 -14.21 REMARK 500 PRO A 139 -87.32 -21.88 REMARK 500 GLU A 180 30.28 -75.46 REMARK 500 PRO A 208 145.76 -39.59 REMARK 500 SER A 210 144.73 -174.10 REMARK 500 ASN A 238 165.46 -49.44 REMARK 500 GLU A 277 10.61 -60.13 REMARK 500 ASP A 303 91.14 -59.92 REMARK 500 ALA A 363 -126.17 -81.45 REMARK 500 MET A 408 127.83 -38.26 REMARK 500 PRO B 23 0.20 -67.96 REMARK 500 ALA B 31 71.15 -118.18 REMARK 500 LYS B 32 -66.40 152.44 REMARK 500 VAL B 63 97.38 -69.15 REMARK 500 LYS B 84 -34.53 -37.01 REMARK 500 SER B 102 117.02 -160.04 REMARK 500 THR B 124 50.51 -113.02 REMARK 500 ASP B 125 109.45 -166.65 REMARK 500 LYS B 130 -51.58 -10.14 REMARK 500 PRO B 139 -72.13 -19.34 REMARK 500 LYS B 151 59.47 -100.56 REMARK 500 VAL B 159 -35.97 -38.51 REMARK 500 LYS B 173 55.72 82.64 REMARK 500 ILE B 174 -77.75 -87.34 REMARK 500 GLU B 180 35.67 -75.52 REMARK 500 ARG B 181 134.37 -170.48 REMARK 500 PRO B 208 150.05 -47.51 REMARK 500 ASP B 218 150.77 -45.71 REMARK 500 ASP B 220 59.17 32.01 REMARK 500 GLU B 277 41.12 -79.38 REMARK 500 ARG B 334 135.99 -35.70 REMARK 500 PRO B 340 116.57 -35.94 REMARK 500 ASP B 357 16.77 53.16 REMARK 500 ALA B 363 -130.92 -74.67 REMARK 500 MET B 408 109.87 -35.39 REMARK 500 LYS B 417 -30.49 -39.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 31 LYS A 32 130.53 REMARK 500 ALA A 138 PRO A 139 43.16 REMARK 500 PRO A 139 ILE A 140 -73.71 REMARK 500 ASN A 238 GLU A 239 141.62 REMARK 500 PHE A 371 THR A 372 149.72 REMARK 500 ALA B 31 LYS B 32 134.11 REMARK 500 ASP B 50 VAL B 51 -149.62 REMARK 500 ALA B 138 PRO B 139 38.56 REMARK 500 PRO B 139 ILE B 140 -102.33 REMARK 500 LYS B 173 ILE B 174 -122.61 REMARK 500 ILE B 174 PHE B 175 132.98 REMARK 500 SER B 179 GLU B 180 130.15 REMARK 500 PRO B 337 GLU B 338 -114.86 REMARK 500 GLU B 338 LYS B 339 138.18 REMARK 500 LYS B 339 PRO B 340 141.94 REMARK 500 PRO B 340 GLU B 341 145.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YW2 RELATED DB: PDB REMARK 900 GAR SYNTHETASE FROM AQUIFEX AEOLICUS REMARK 900 RELATED ID: AAE001000742.2 RELATED DB: TARGETDB DBREF 2YYA A 1 424 UNP O66949 PUR2_AQUAE 1 424 DBREF 2YYA B 1 424 UNP O66949 PUR2_AQUAE 1 424 SEQRES 1 A 424 MET LYS VAL LEU VAL VAL GLY ASN GLY GLY ARG GLU HIS SEQRES 2 A 424 ALA ILE ALA TRP LYS VAL ALA GLN SER PRO LEU VAL LYS SEQRES 3 A 424 GLU LEU TYR VAL ALA LYS GLY ASN ALA GLY ILE TRP GLU SEQRES 4 A 424 ILE ALA LYS ARG VAL ASP ILE SER PRO THR ASP VAL GLU SEQRES 5 A 424 LYS LEU ALA GLU PHE ALA LYS ASN GLU GLY VAL ASP PHE SEQRES 6 A 424 THR ILE VAL GLY PRO GLU ALA PRO LEU VAL GLU GLY ILE SEQRES 7 A 424 VAL ASP GLU PHE GLU LYS ARG GLY LEU LYS ILE PHE GLY SEQRES 8 A 424 PRO ASN LYS GLU ALA ALA LYS LEU GLU GLY SER LYS ALA SEQRES 9 A 424 PHE ALA LYS THR PHE MET LYS LYS TYR GLY ILE PRO THR SEQRES 10 A 424 ALA ARG TYR GLU VAL PHE THR ASP PHE GLU LYS ALA LYS SEQRES 11 A 424 GLU TYR VAL GLU LYS VAL GLY ALA PRO ILE VAL VAL LYS SEQRES 12 A 424 ALA ASP GLY LEU ALA ALA GLY LYS GLY ALA VAL VAL CYS SEQRES 13 A 424 GLU THR VAL GLU LYS ALA ILE GLU THR LEU ASP ARG PHE SEQRES 14 A 424 LEU ASN LYS LYS ILE PHE GLY LYS SER SER GLU ARG VAL SEQRES 15 A 424 VAL ILE GLU GLU PHE LEU GLU GLY GLU GLU ALA SER TYR SEQRES 16 A 424 ILE VAL MET ILE ASN GLY ASP ARG TYR VAL PRO LEU PRO SEQRES 17 A 424 THR SER GLN ASP HIS LYS ARG LEU LEU ASP GLU ASP LYS SEQRES 18 A 424 GLY PRO ASN THR GLY GLY MET GLY ALA TYR SER PRO THR SEQRES 19 A 424 PRO VAL ILE ASN GLU GLU VAL GLU LYS ARG ILE ARG GLU SEQRES 20 A 424 GLU ILE VAL GLU ARG VAL ILE LYS GLY LEU LYS GLU GLU SEQRES 21 A 424 GLY ILE TYR TYR ARG GLY PHE LEU TYR ALA GLY LEU MET SEQRES 22 A 424 ILE THR LYS GLU GLY PRO LYS VAL LEU GLU PHE ASN VAL SEQRES 23 A 424 ARG LEU GLY ASP PRO GLU ALA GLN PRO ILE LEU MET ARG SEQRES 24 A 424 VAL LYS ASN ASP PHE LEU GLU THR LEU LEU ASN PHE TYR SEQRES 25 A 424 GLU GLY LYS ASP VAL HIS ILE LYS GLU ASP GLU ARG TYR SEQRES 26 A 424 ALA LEU ASP VAL VAL LEU ALA SER ARG GLY TYR PRO GLU SEQRES 27 A 424 LYS PRO GLU THR GLY LYS ILE ILE HIS GLY LEU ASP TYR SEQRES 28 A 424 LEU LYS SER MET GLU ASP VAL VAL VAL PHE HIS ALA GLY SEQRES 29 A 424 THR LYS LYS GLU GLY ASN PHE THR VAL THR SER GLY GLY SEQRES 30 A 424 ARG VAL LEU ASN VAL CYS ALA TYR GLY LYS THR LEU LYS SEQRES 31 A 424 GLU ALA LYS GLU ARG ALA TYR GLU ALA ILE ARG TYR VAL SEQRES 32 A 424 CYS PHE GLU GLY MET HIS TYR ARG LYS ASP ILE GLY ASP SEQRES 33 A 424 LYS ALA PHE LYS TYR LEU SER GLU SEQRES 1 B 424 MET LYS VAL LEU VAL VAL GLY ASN GLY GLY ARG GLU HIS SEQRES 2 B 424 ALA ILE ALA TRP LYS VAL ALA GLN SER PRO LEU VAL LYS SEQRES 3 B 424 GLU LEU TYR VAL ALA LYS GLY ASN ALA GLY ILE TRP GLU SEQRES 4 B 424 ILE ALA LYS ARG VAL ASP ILE SER PRO THR ASP VAL GLU SEQRES 5 B 424 LYS LEU ALA GLU PHE ALA LYS ASN GLU GLY VAL ASP PHE SEQRES 6 B 424 THR ILE VAL GLY PRO GLU ALA PRO LEU VAL GLU GLY ILE SEQRES 7 B 424 VAL ASP GLU PHE GLU LYS ARG GLY LEU LYS ILE PHE GLY SEQRES 8 B 424 PRO ASN LYS GLU ALA ALA LYS LEU GLU GLY SER LYS ALA SEQRES 9 B 424 PHE ALA LYS THR PHE MET LYS LYS TYR GLY ILE PRO THR SEQRES 10 B 424 ALA ARG TYR GLU VAL PHE THR ASP PHE GLU LYS ALA LYS SEQRES 11 B 424 GLU TYR VAL GLU LYS VAL GLY ALA PRO ILE VAL VAL LYS SEQRES 12 B 424 ALA ASP GLY LEU ALA ALA GLY LYS GLY ALA VAL VAL CYS SEQRES 13 B 424 GLU THR VAL GLU LYS ALA ILE GLU THR LEU ASP ARG PHE SEQRES 14 B 424 LEU ASN LYS LYS ILE PHE GLY LYS SER SER GLU ARG VAL SEQRES 15 B 424 VAL ILE GLU GLU PHE LEU GLU GLY GLU GLU ALA SER TYR SEQRES 16 B 424 ILE VAL MET ILE ASN GLY ASP ARG TYR VAL PRO LEU PRO SEQRES 17 B 424 THR SER GLN ASP HIS LYS ARG LEU LEU ASP GLU ASP LYS SEQRES 18 B 424 GLY PRO ASN THR GLY GLY MET GLY ALA TYR SER PRO THR SEQRES 19 B 424 PRO VAL ILE ASN GLU GLU VAL GLU LYS ARG ILE ARG GLU SEQRES 20 B 424 GLU ILE VAL GLU ARG VAL ILE LYS GLY LEU LYS GLU GLU SEQRES 21 B 424 GLY ILE TYR TYR ARG GLY PHE LEU TYR ALA GLY LEU MET SEQRES 22 B 424 ILE THR LYS GLU GLY PRO LYS VAL LEU GLU PHE ASN VAL SEQRES 23 B 424 ARG LEU GLY ASP PRO GLU ALA GLN PRO ILE LEU MET ARG SEQRES 24 B 424 VAL LYS ASN ASP PHE LEU GLU THR LEU LEU ASN PHE TYR SEQRES 25 B 424 GLU GLY LYS ASP VAL HIS ILE LYS GLU ASP GLU ARG TYR SEQRES 26 B 424 ALA LEU ASP VAL VAL LEU ALA SER ARG GLY TYR PRO GLU SEQRES 27 B 424 LYS PRO GLU THR GLY LYS ILE ILE HIS GLY LEU ASP TYR SEQRES 28 B 424 LEU LYS SER MET GLU ASP VAL VAL VAL PHE HIS ALA GLY SEQRES 29 B 424 THR LYS LYS GLU GLY ASN PHE THR VAL THR SER GLY GLY SEQRES 30 B 424 ARG VAL LEU ASN VAL CYS ALA TYR GLY LYS THR LEU LYS SEQRES 31 B 424 GLU ALA LYS GLU ARG ALA TYR GLU ALA ILE ARG TYR VAL SEQRES 32 B 424 CYS PHE GLU GLY MET HIS TYR ARG LYS ASP ILE GLY ASP SEQRES 33 B 424 LYS ALA PHE LYS TYR LEU SER GLU FORMUL 3 HOH *89(H2 O) HELIX 1 1 GLY A 9 ALA A 20 1 12 HELIX 2 2 GLY A 36 ILE A 40 5 5 HELIX 3 3 ASP A 50 GLY A 62 1 13 HELIX 4 4 PRO A 70 GLU A 76 1 7 HELIX 5 5 GLY A 77 ARG A 85 1 9 HELIX 6 6 ALA A 97 SER A 102 1 6 HELIX 7 7 SER A 102 LYS A 112 1 11 HELIX 8 8 ASP A 125 GLY A 137 1 13 HELIX 9 9 THR A 158 ASN A 171 1 14 HELIX 10 10 PHE A 175 SER A 179 5 5 HELIX 11 11 ASN A 238 ILE A 249 1 12 HELIX 12 12 ILE A 249 GLU A 260 1 12 HELIX 13 13 GLU A 292 ARG A 299 1 8 HELIX 14 14 ASP A 303 GLU A 313 1 11 HELIX 15 15 GLY A 348 LYS A 353 1 6 HELIX 16 16 THR A 388 ARG A 401 1 14 HELIX 17 17 GLY A 415 PHE A 419 5 5 HELIX 18 18 GLY B 9 ALA B 20 1 12 HELIX 19 19 GLY B 36 ILE B 40 5 5 HELIX 20 20 ASP B 50 GLY B 62 1 13 HELIX 21 21 GLU B 71 GLU B 76 1 6 HELIX 22 22 GLY B 77 ARG B 85 1 9 HELIX 23 23 ALA B 97 SER B 102 1 6 HELIX 24 24 SER B 102 GLY B 114 1 13 HELIX 25 25 ASP B 125 GLU B 134 1 10 HELIX 26 26 THR B 158 ASN B 171 1 14 HELIX 27 27 ASN B 238 ILE B 249 1 12 HELIX 28 28 ILE B 249 GLU B 260 1 12 HELIX 29 29 GLU B 292 ARG B 299 1 8 HELIX 30 30 ASP B 303 GLU B 313 1 11 HELIX 31 31 TYR B 351 MET B 355 5 5 HELIX 32 32 THR B 388 ARG B 401 1 14 HELIX 33 33 GLY B 415 LEU B 422 5 8 SHEET 1 A 5 LYS A 42 VAL A 44 0 SHEET 2 A 5 GLU A 27 LYS A 32 1 N VAL A 30 O LYS A 42 SHEET 3 A 5 LYS A 2 GLY A 7 1 N VAL A 3 O GLU A 27 SHEET 4 A 5 PHE A 65 VAL A 68 1 O ILE A 67 N VAL A 6 SHEET 5 A 5 ILE A 89 PHE A 90 1 O PHE A 90 N THR A 66 SHEET 1 B 4 TYR A 120 GLU A 121 0 SHEET 2 B 4 ILE A 184 GLU A 185 -1 O ILE A 184 N GLU A 121 SHEET 3 B 4 VAL A 141 LYS A 143 -1 N VAL A 141 O GLU A 185 SHEET 4 B 4 ALA A 153 VAL A 155 -1 O VAL A 154 N VAL A 142 SHEET 1 C 8 GLY A 278 ASN A 285 0 SHEET 2 C 8 ARG A 265 THR A 275 -1 N GLY A 271 O GLU A 283 SHEET 3 C 8 GLU A 191 ASN A 200 -1 N GLU A 191 O ILE A 274 SHEET 4 C 8 ARG A 203 ASP A 212 -1 O VAL A 205 N MET A 198 SHEET 5 C 8 GLY A 229 SER A 232 -1 O TYR A 231 N GLN A 211 SHEET 6 C 8 TYR A 325 ALA A 332 -1 O ASP A 328 N ALA A 230 SHEET 7 C 8 ARG A 378 GLY A 386 -1 O VAL A 382 N VAL A 329 SHEET 8 C 8 VAL A 358 HIS A 362 -1 N VAL A 359 O CYS A 383 SHEET 1 D 2 ARG A 215 LEU A 217 0 SHEET 2 D 2 LYS A 221 ASN A 224 -1 O LYS A 221 N LEU A 217 SHEET 1 E 2 THR A 365 GLU A 368 0 SHEET 2 E 2 PHE A 371 THR A 374 -1 O PHE A 371 N GLU A 368 SHEET 1 F 5 LYS B 42 VAL B 44 0 SHEET 2 F 5 GLU B 27 ALA B 31 1 N VAL B 30 O LYS B 42 SHEET 3 F 5 LYS B 2 VAL B 6 1 N VAL B 3 O GLU B 27 SHEET 4 F 5 PHE B 65 VAL B 68 1 O ILE B 67 N VAL B 6 SHEET 5 F 5 ILE B 89 PHE B 90 1 O PHE B 90 N THR B 66 SHEET 1 G 4 TYR B 120 PHE B 123 0 SHEET 2 G 4 VAL B 182 GLU B 185 -1 O ILE B 184 N GLU B 121 SHEET 3 G 4 VAL B 141 ALA B 144 -1 N LYS B 143 O VAL B 183 SHEET 4 G 4 ALA B 153 VAL B 155 -1 O VAL B 154 N VAL B 142 SHEET 1 H 4 ARG B 203 PRO B 206 0 SHEET 2 H 4 GLY B 190 ASN B 200 -1 N MET B 198 O VAL B 205 SHEET 3 H 4 ARG B 265 THR B 275 -1 O GLY B 266 N ILE B 199 SHEET 4 H 4 GLY B 278 ASN B 285 -1 O LEU B 282 N GLY B 271 SHEET 1 I 5 GLN B 211 ASP B 212 0 SHEET 2 I 5 GLY B 229 SER B 232 -1 O TYR B 231 N GLN B 211 SHEET 3 I 5 TYR B 325 ALA B 332 -1 O ASP B 328 N ALA B 230 SHEET 4 I 5 ARG B 378 GLY B 386 -1 O VAL B 382 N VAL B 329 SHEET 5 I 5 VAL B 358 HIS B 362 -1 N VAL B 359 O CYS B 383 SHEET 1 J 2 ARG B 215 LEU B 217 0 SHEET 2 J 2 LYS B 221 ASN B 224 -1 O LYS B 221 N LEU B 217 SHEET 1 K 2 THR B 365 GLU B 368 0 SHEET 2 K 2 PHE B 371 THR B 374 -1 O PHE B 371 N GLU B 368 SSBOND 1 CYS A 404 CYS B 404 1555 1655 2.99 CISPEP 1 SER A 232 PRO A 233 0 -3.55 CISPEP 2 ASP A 290 PRO A 291 0 19.56 CISPEP 3 TYR A 336 PRO A 337 0 6.13 CISPEP 4 SER B 232 PRO B 233 0 -12.30 CISPEP 5 ASP B 290 PRO B 291 0 19.36 CISPEP 6 TYR B 336 PRO B 337 0 -3.89 CRYST1 97.262 45.152 103.484 90.00 103.87 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 0.010282 0.000000 0.002539 0.00000 SCALE2 0.000000 0.022147 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009954 0.00000