PDB Short entry for 1DGD HEADER LYASE 29-JUN-94 1DGD TITLE AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE TITLE 2 OF DIALKYLGLYCINE DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIALKYLGLYCINE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.1.64; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CEPACIA; SOURCE 3 ORGANISM_TAXID: 292 KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR E.HOHENESTER,J.N.JANSONIUS REVDAT 4 29-NOV-17 1DGD 1 REMARK HELIX REVDAT 3 13-JUL-11 1DGD 1 VERSN REVDAT 2 24-FEB-09 1DGD 1 VERSN REVDAT 1 30-SEP-94 1DGD 0 JRNL AUTH E.HOHENESTER,J.W.KELLER,J.N.JANSONIUS JRNL TITL AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE JRNL TITL 2 STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE. JRNL REF BIOCHEMISTRY V. 33 13561 1994 JRNL REFN ISSN 0006-2960 JRNL PMID 7947767 JRNL DOI 10.1021/BI00250A008 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.D.TONEY,E.HOHENESTER,S.W.JACOB,J.N.JANSONIUS REMARK 1 TITL DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE REMARK 1 TITL 2 SITE AND ALKALI METAL SITES REMARK 1 REF SCIENCE V. 261 756 1993 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.W.KELLER,K.B.BAURICK,G.C.RUTT,M.V.O'MALLEY,N.L.SONAFRANK, REMARK 1 AUTH 2 R.REYNOLDS,L.O.EBBESSON,F.F.VAJDOS REMARK 1 TITL PSEUDOMONAS CEPACIA 2,2-DIALKYLGLYCINE DECARBOXYLASE. REMARK 1 TITL 2 SEQUENCE AND EXPRESSION IN ESCHERICHIA COLI OF STRUCTURAL REMARK 1 TITL 3 AND REPRESSOR GENES REMARK 1 REF J.BIOL.CHEM. V. 265 5531 1990 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14224 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.600 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : 0.009 ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 1.700 ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DGD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 28.86667 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 57.73333 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.86667 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 57.73333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.86667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 57.73333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 28.86667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 57.73333 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: THE MOLECULE IS A TETRAMER OF IDENTICAL SUBUNITS. THIS REMARK 300 ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH REMARK 300 COMPRISES ONE MONOMER. THE TETRAMER CAN BE GENERATED BY REMARK 300 CRYSTALLOGRAPHIC DYADS. APPLYING THE FOLLOWING REMARK 300 TRANSFORMATION TO THE COORDINATES IN THIS ENTRY WILL YIELD REMARK 300 A DIMER: REMARK 300 REMARK 300 MTRIX1 1 -0.500000 0.866000 0.000000 0.00000 REMARK 300 MTRIX2 1 0.866000 0.500000 0.000000 0.00000 REMARK 300 MTRIX3 1 0.000000 0.000000 1.000000 28.87000 REMARK 300 REMARK 300 APPLYING THE FOLLOWING TRANSFORMATION TO THE DIMER WILL REMARK 300 YIELD THE TETRAMER: REMARK 300 REMARK 300 MTRIX1 2 -1.000000 0.000000 0.000000 76.40000 REMARK 300 MTRIX2 2 0.000000 -1.000000 0.000000 132.20000 REMARK 300 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 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: TETRAMERIC 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 -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 28.86667 REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 76.35000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 132.24208 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 28.86667 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 76.35000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 132.24208 REMARK 350 BIOMT3 4 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 SER A 2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 11 CD NE CZ NH1 NH2 REMARK 480 ARG A 14 CG CD NE CZ NH1 NH2 REMARK 480 HIS A 15 CG ND1 CD2 CE1 NE2 REMARK 480 ARG A 43 NE CZ NH1 NH2 REMARK 480 ARG A 176 NE CZ NH1 NH2 REMARK 480 ARG A 179 NE CZ NH1 NH2 REMARK 480 ASN A 180 CG OD1 ND2 REMARK 480 ASP A 223 CG OD1 OD2 REMARK 480 GLU A 295 CG CD OE1 OE2 REMARK 480 ARG A 339 CD NE CZ NH1 NH2 REMARK 480 GLU A 346 CD OE1 OE2 REMARK 480 ARG A 347 CB CG CD NE CZ NH1 NH2 REMARK 480 LYS A 367 CG CD CE NZ REMARK 480 ASP A 368 CG OD1 OD2 REMARK 480 ARG A 370 CB CG CD NE CZ NH1 NH2 REMARK 480 GLU A 373 CG CD OE1 OE2 REMARK 480 ASP A 376 CB CG OD1 OD2 REMARK 480 GLU A 430 CG CD OE1 OE2 REMARK 480 ARG A 431 NE CZ NH1 NH2 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 GLU A 30 CD GLU A 30 OE2 0.068 REMARK 500 GLU A 63 CD GLU A 63 OE2 0.069 REMARK 500 GLU A 70 CD GLU A 70 OE2 0.081 REMARK 500 GLU A 113 CD GLU A 113 OE1 0.073 REMARK 500 GLU A 116 CD GLU A 116 OE1 0.091 REMARK 500 GLU A 178 CD GLU A 178 OE2 0.099 REMARK 500 GLU A 220 CD GLU A 220 OE1 0.088 REMARK 500 GLU A 291 CD GLU A 291 OE1 0.077 REMARK 500 GLU A 385 CD GLU A 385 OE1 0.085 REMARK 500 GLU A 415 CD GLU A 415 OE1 0.079 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 ARG A 19 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 41 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 47 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 89 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 89 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 93 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 103 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 PRO A 175 C - N - CD ANGL. DEV. = -15.8 DEGREES REMARK 500 ASP A 184 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 190 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 190 CB - CG - OD2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ASP A 197 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 223 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 MET A 226 CA - CB - CG ANGL. DEV. = -13.7 DEGREES REMARK 500 ASP A 307 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 307 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 319 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 323 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 323 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ASP A 324 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 343 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 343 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 349 CB - CG - OD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 368 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 368 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 419 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 419 CB - CG - OD2 ANGL. DEV. = -6.4 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 ASP A 5 47.06 -92.09 REMARK 500 PRO A 26 47.16 -90.78 REMARK 500 GLN A 52 59.58 -96.69 REMARK 500 ALA A 55 61.16 -52.91 REMARK 500 LEU A 108 -157.28 -119.62 REMARK 500 SER A 271 -80.63 -167.00 REMARK 500 PHE A 300 88.15 -153.03 REMARK 500 LEU A 359 41.58 -107.77 REMARK 500 ALA A 408 77.46 -166.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 LI A 436 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 435 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 95 O REMARK 620 2 LEU A 102 O 91.8 REMARK 620 3 HOH A 540 O 90.8 85.3 REMARK 620 4 PRO A 99 O 165.7 101.3 95.9 REMARK 620 5 THR A 98 O 90.1 156.5 118.0 75.7 REMARK 620 6 THR A 98 OG1 71.6 84.6 159.4 103.7 73.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LI A 436 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 552 O REMARK 620 2 LEU A 78 O 96.5 REMARK 620 3 HOH A 539 O 112.9 96.5 REMARK 620 4 ASP A 307 OD1 128.2 118.9 100.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ACTIVE SITE: THE COFACTOR PLP IS COVALENTLY REMARK 800 BOUND REMARK 800 REMARK 800 SITE_IDENTIFIER: ME1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE 1 (NEAR THE ACTIVE SITE): REMARK 800 LIGANDS TO THE LI+ ION ARE INDICATED REMARK 800 REMARK 800 SITE_IDENTIFIER: ME2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE 2: LIGANDS TO THE NA+ ION ARE REMARK 800 INDICATED REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 435 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 434 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: DGDA_BURCE REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 999 GLN 14 HIS 15 REMARK 999 GLU 51 GLN 52 REMARK 999 ILE 81 MET 82 REMARK 999 VAL 82 LEU 83 REMARK 999 ARG 307 PRO 308 REMARK 999 PRO 309 LEU 309 REMARK 999 GLY 312 ALA 312 REMARK 999 REMARK 999 THE PUBLISHED AMINO ACID SEQUENCE (REFERENCE 1) WAS REMARK 999 CORRECTED AT THREE POSITIONS. RESEQUENCING OF SEVERAL REMARK 999 GC-RICH REGIONS OF THE DGDA GENE VERIFIED THESE CHANGES REMARK 999 (J.W. KELLER, PERSONAL COMMUNICATION): REMARK 999 GLU 52 --> GLN 52 REMARK 999 ILE 82, VAL 83 --> MET 82, LEU 83 REMARK 999 ARG 308, CYS 309, PRO 310, PRO 311, ALA 312, GLY 313 --> REMARK 999 PRO 308, LEU 309, PRO 310, ALA 311, ALA 312 (INCLUDES REMARK 999 A DELETION). REMARK 999 GLN 15 -->HIS 15 (M.D. TONEY ET AL., J. MOL. BIOL. 222: REMARK 999 873-875 (1991)). DBREF 1DGD A 2 433 UNP P16932 DGDA_BURCE 1 432 SEQADV 1DGD HIS A 15 UNP P16932 GLN 14 CONFLICT SEQRES 1 A 432 SER LEU ASN ASP ASP ALA THR PHE TRP ARG ASN ALA ARG SEQRES 2 A 432 HIS HIS LEU VAL ARG TYR GLY GLY THR PHE GLU PRO MET SEQRES 3 A 432 ILE ILE GLU ARG ALA LYS GLY SER PHE VAL TYR ASP ALA SEQRES 4 A 432 ASP GLY ARG ALA ILE LEU ASP PHE THR SER GLY GLN MET SEQRES 5 A 432 SER ALA VAL LEU GLY HIS CYS HIS PRO GLU ILE VAL SER SEQRES 6 A 432 VAL ILE GLY GLU TYR ALA GLY LYS LEU ASP HIS LEU PHE SEQRES 7 A 432 SER GLY MET LEU SER ARG PRO VAL VAL ASP LEU ALA THR SEQRES 8 A 432 ARG LEU ALA ASN ILE THR PRO PRO GLY LEU ASP ARG ALA SEQRES 9 A 432 LEU LEU LEU SER THR GLY ALA GLU SER ASN GLU ALA ALA SEQRES 10 A 432 ILE ARG MET ALA LYS LEU VAL THR GLY LYS TYR GLU ILE SEQRES 11 A 432 VAL GLY PHE ALA GLN SER TRP HIS GLY MET THR GLY ALA SEQRES 12 A 432 ALA ALA SER ALA THR TYR SER ALA GLY ARG LYS GLY VAL SEQRES 13 A 432 GLY PRO ALA ALA VAL GLY SER PHE ALA ILE PRO ALA PRO SEQRES 14 A 432 PHE THR TYR ARG PRO ARG PHE GLU ARG ASN GLY ALA TYR SEQRES 15 A 432 ASP TYR LEU ALA GLU LEU ASP TYR ALA PHE ASP LEU ILE SEQRES 16 A 432 ASP ARG GLN SER SER GLY ASN LEU ALA ALA PHE ILE ALA SEQRES 17 A 432 GLU PRO ILE LEU SER SER GLY GLY ILE ILE GLU LEU PRO SEQRES 18 A 432 ASP GLY TYR MET ALA ALA LEU LYS ARG LYS CYS GLU ALA SEQRES 19 A 432 ARG GLY MET LEU LEU ILE LEU ASP GLU ALA GLN THR GLY SEQRES 20 A 432 VAL GLY ARG THR GLY THR MET PHE ALA CYS GLN ARG ASP SEQRES 21 A 432 GLY VAL THR PRO ASP ILE LEU THR LEU SER LYS THR LEU SEQRES 22 A 432 GLY ALA GLY LEU PRO LEU ALA ALA ILE VAL THR SER ALA SEQRES 23 A 432 ALA ILE GLU GLU ARG ALA HIS GLU LEU GLY TYR LEU PHE SEQRES 24 A 432 TYR THR THR HIS VAL SER ASP PRO LEU PRO ALA ALA VAL SEQRES 25 A 432 GLY LEU ARG VAL LEU ASP VAL VAL GLN ARG ASP GLY LEU SEQRES 26 A 432 VAL ALA ARG ALA ASN VAL MET GLY ASP ARG LEU ARG ARG SEQRES 27 A 432 GLY LEU LEU ASP LEU MET GLU ARG PHE ASP CYS ILE GLY SEQRES 28 A 432 ASP VAL ARG GLY ARG GLY LEU LEU LEU GLY VAL GLU ILE SEQRES 29 A 432 VAL LYS ASP ARG ARG THR LYS GLU PRO ALA ASP GLY LEU SEQRES 30 A 432 GLY ALA LYS ILE THR ARG GLU CYS MET ASN LEU GLY LEU SEQRES 31 A 432 SER MET ASN ILE VAL GLN LEU PRO GLY MET GLY GLY VAL SEQRES 32 A 432 PHE ARG ILE ALA PRO PRO LEU THR VAL SER GLU ASP GLU SEQRES 33 A 432 ILE ASP LEU GLY LEU SER LEU LEU GLY GLN ALA ILE GLU SEQRES 34 A 432 ARG ALA LEU HET NA A 435 1 HET LI A 436 1 HET PLP A 437 15 HET MES A 434 12 HETNAM NA SODIUM ION HETNAM LI LITHIUM ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 NA NA 1+ FORMUL 3 LI LI 1+ FORMUL 4 PLP C8 H10 N O6 P FORMUL 5 MES C6 H13 N O4 S FORMUL 6 HOH *99(H2 O) HELIX 1 H1 ALA A 7 HIS A 16 1 10 HELIX 2 H2 PRO A 62 ALA A 72 1 11 HELIX 3 H3 ARG A 85 ILE A 97 1 13 HELIX 4 H4 GLY A 111 THR A 126 1 16 HELIX 5 H5 GLY A 143 SER A 147 1 5 HELIX 6 H6 TYR A 185 GLN A 199 1 15 HELIX 7 H7 TYR A 225 ALA A 235 1 11 HELIX 8 H8 ALA A 257 ASP A 261 1 5 HELIX 9 H9 ALA A 287 LEU A 296 1 10 HELIX 10 H10 PRO A 308 ARG A 323 1 16 HELIX 11 H11 LEU A 326 ARG A 347 1 22 HELIX 12 H12 LEU A 378 LEU A 389 1 12 HELIX 13 H13 GLU A 415 ARG A 431 1 17 SHEET 1 S1 3 GLU A 30 LYS A 33 0 SHEET 2 S1 3 PHE A 36 ASP A 39 -1 N TYR A 38 O LYS A 33 SHEET 3 S1 3 ARG A 43 ASP A 47 -1 N ILE A 45 O VAL A 37 SHEET 1 S2 7 ARG A 104 SER A 109 0 SHEET 2 S2 7 LEU A 280 THR A 285 -1 O THR A 285 N ARG A 104 SHEET 3 S2 7 ASP A 266 LEU A 270 -1 N LEU A 268 O VAL A 284 SHEET 4 S2 7 LEU A 239 GLU A 244 1 N LEU A 242 O ILE A 267 SHEET 5 S2 7 LEU A 204 ALA A 209 1 N ALA A 209 O ILE A 241 SHEET 6 S2 7 GLU A 130 PHE A 134 1 O VAL A 132 N ILE A 208 SHEET 7 S2 7 GLY A 163 ILE A 167 1 O PHE A 165 N GLY A 133 LINK NZ LYS A 272 C4A PLP A 437 1555 1555 1.30 LINK NA NA A 435 O ALA A 95 1555 1555 2.43 LINK NA NA A 435 O LEU A 102 1555 1555 2.42 LINK NA NA A 435 O HOH A 540 1555 1555 2.29 LINK NA NA A 435 O PRO A 99 1555 1555 2.23 LINK NA NA A 435 O THR A 98 1555 1555 2.41 LINK LI LI A 436 O HOH A 552 1555 1555 1.92 LINK LI LI A 436 O LEU A 78 1555 1555 1.92 LINK LI LI A 436 O HOH A 539 1555 1555 1.90 LINK LI LI A 436 OD1 ASP A 307 1555 1555 1.87 LINK OG1 THR A 98 NA NA A 435 1555 1555 2.86 SITE 1 ACT 22 GLN A 52 MET A 53 PHE A 79 THR A 110 SITE 2 ACT 22 GLY A 111 ASN A 115 SER A 137 TRP A 138 SITE 3 ACT 22 MET A 141 GLU A 210 SER A 214 SER A 215 SITE 4 ACT 22 ASP A 243 ALA A 245 GLN A 246 LYS A 272 SITE 5 ACT 22 PLP A 437 TYR A 301 THR A 303 ASN A 394 SITE 6 ACT 22 ARG A 406 MES A 434 SITE 1 ME1 5 LEU A 78 ASP A 307 HOH A 539 HOH A 552 SITE 2 ME1 5 LI A 436 SITE 1 ME2 6 ALA A 95 THR A 98 PRO A 99 LEU A 102 SITE 2 ME2 6 HOH A 540 NA A 435 SITE 1 AC1 5 ALA A 95 THR A 98 PRO A 99 LEU A 102 SITE 2 AC1 5 HOH A 540 SITE 1 AC2 16 THR A 110 GLY A 111 ALA A 112 ASN A 115 SITE 2 AC2 16 TRP A 138 HIS A 139 GLU A 210 ASP A 243 SITE 3 AC2 16 ALA A 245 GLN A 246 LYS A 272 THR A 302 SITE 4 AC2 16 THR A 303 MES A 434 HOH A 555 HOH A 557 SITE 1 AC3 8 GLN A 52 TRP A 138 ALA A 152 SER A 215 SITE 2 AC3 8 GLN A 246 LYS A 272 ARG A 406 PLP A 437 CRYST1 152.700 152.700 86.600 90.00 90.00 120.00 P 64 2 2 12 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 0.006549 0.003781 0.000000 0.00000 SCALE2 0.000000 0.007562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011547 0.00000