HEADER LYASE 12-MAY-05 1ZOB TITLE CRYSTAL STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASES BOUND WITH CALCIUM TITLE 2 ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,2-DIALKYLGLYCINE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DGD; COMPND 5 EC: 4.1.1.64; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CEPACIA; SOURCE 3 ORGANISM_TAXID: 292; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBTAC KEYWDS DECARBOXYLASE, PYRIDOXAL PHOSPHATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR W.LIU,M.D.TONEY REVDAT 4 23-AUG-23 1ZOB 1 REMARK LINK REVDAT 3 13-JUL-11 1ZOB 1 VERSN REVDAT 2 24-FEB-09 1ZOB 1 VERSN REVDAT 1 08-AUG-06 1ZOB 0 JRNL AUTH W.LIU,M.D.TONEY JRNL TITL CRYSTAL STRUCTURES OF DIALKYLGLYCINE DECARBOXYLASE BOUND JRNL TITL 2 WITH CESIUM ION AND CALCIUM ION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14257 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 725 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3252 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZOB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14258 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 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 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1DKA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4K, MES, PLP, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 28.23433 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 56.46867 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 28.23433 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 56.46867 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 28.23433 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 56.46867 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 28.23433 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 56.46867 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE SIX FOLD AXIS: Y, X, 1/3-Z 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 28840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -196.0 KCAL/MOL 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 75.27650 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 130.38272 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 28.23433 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 75.27650 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 130.38272 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 28.23433 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 MET A 1 REMARK 465 SER A 2 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 NZ LYS A 381 NZ LYS A 381 11556 2.16 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 6 90.93 -20.74 REMARK 500 TYR A 20 30.72 -94.12 REMARK 500 PRO A 26 38.39 -80.61 REMARK 500 PHE A 48 31.32 -91.84 REMARK 500 GLN A 52 61.41 -115.75 REMARK 500 SER A 54 -81.89 -98.52 REMARK 500 ALA A 55 78.85 -37.02 REMARK 500 CYS A 60 53.66 37.08 REMARK 500 ASP A 76 -66.61 -120.04 REMARK 500 PRO A 99 141.21 -38.79 REMARK 500 LEU A 108 -156.04 -122.86 REMARK 500 PRO A 159 160.66 -49.79 REMARK 500 LEU A 213 98.40 -68.72 REMARK 500 GLU A 244 43.44 -102.06 REMARK 500 SER A 271 -84.14 -168.35 REMARK 500 PRO A 279 89.88 -59.81 REMARK 500 ALA A 282 162.69 179.79 REMARK 500 PHE A 300 79.44 -159.36 REMARK 500 SER A 306 36.04 71.59 REMARK 500 ARG A 357 146.63 -172.25 REMARK 500 ASP A 368 118.42 -161.19 REMARK 500 REMARK 500 REMARK: NULL 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 CA A 436 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 78 O REMARK 620 2 VAL A 305 O 159.5 REMARK 620 3 ASP A 307 OD1 77.6 114.8 REMARK 620 4 HOH A 481 O 92.7 67.9 111.2 REMARK 620 5 HOH A 482 O 98.8 86.7 126.7 122.0 REMARK 620 N 1 2 3 4 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 THR A 98 O 93.7 REMARK 620 3 THR A 98 OG1 72.1 70.9 REMARK 620 4 PRO A 99 O 152.1 61.3 87.2 REMARK 620 5 LEU A 102 O 90.8 140.0 72.9 100.9 REMARK 620 6 HOH A 500 O 108.8 109.2 179.1 92.1 106.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE 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 CA A 436 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 437 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DKA RELATED DB: PDB REMARK 900 DIALKYLGLYCINE DECARBOXYLASE COMPLEX WITH POTASSIUM ION REMARK 900 RELATED ID: 2DKB RELATED DB: PDB REMARK 900 DIALKYLGLYCINE DECARBOXYLASE COMPLEX WITH SODIUM ION REMARK 900 RELATED ID: 1ZOD RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHOR HIS15 AND GLU81 ARE NATIVE REMARK 999 RESIDUES IN THE PROTEIN AND THERE IS AN ERROR IN THE REMARK 999 DATABASE SEQUENCE DUE TO THE MISTAKE IN THE INITIAL REMARK 999 PROTEIN SEQUENCING. DBREF 1ZOB A 1 433 UNP P16932 DGDA_BURCE 1 432 SEQADV 1ZOB HIS A 15 UNP P16932 GLN 14 SEE REMARK 999 SEQADV 1ZOB GLU A 81 UNP P16932 GLY 80 SEE REMARK 999 SEQRES 1 A 433 MET SER LEU ASN ASP ASP ALA THR PHE TRP ARG ASN ALA SEQRES 2 A 433 ARG HIS HIS LEU VAL ARG TYR GLY GLY THR PHE GLU PRO SEQRES 3 A 433 MET ILE ILE GLU ARG ALA LYS GLY SER PHE VAL TYR ASP SEQRES 4 A 433 ALA ASP GLY ARG ALA ILE LEU ASP PHE THR SER GLY GLN SEQRES 5 A 433 MET SER ALA VAL LEU GLY HIS CYS HIS PRO GLU ILE VAL SEQRES 6 A 433 SER VAL ILE GLY GLU TYR ALA GLY LYS LEU ASP HIS LEU SEQRES 7 A 433 PHE SER GLU MET LEU SER ARG PRO VAL VAL ASP LEU ALA SEQRES 8 A 433 THR ARG LEU ALA ASN ILE THR PRO PRO GLY LEU ASP ARG SEQRES 9 A 433 ALA LEU LEU LEU SER THR GLY ALA GLU SER ASN GLU ALA SEQRES 10 A 433 ALA ILE ARG MET ALA LYS LEU VAL THR GLY LYS TYR GLU SEQRES 11 A 433 ILE VAL GLY PHE ALA GLN SER TRP HIS GLY MET THR GLY SEQRES 12 A 433 ALA ALA ALA SER ALA THR TYR SER ALA GLY ARG LYS GLY SEQRES 13 A 433 VAL GLY PRO ALA ALA VAL GLY SER PHE ALA ILE PRO ALA SEQRES 14 A 433 PRO PHE THR TYR ARG PRO ARG PHE GLU ARG ASN GLY ALA SEQRES 15 A 433 TYR ASP TYR LEU ALA GLU LEU ASP TYR ALA PHE ASP LEU SEQRES 16 A 433 ILE ASP ARG GLN SER SER GLY ASN LEU ALA ALA PHE ILE SEQRES 17 A 433 ALA GLU PRO ILE LEU SER SER GLY GLY ILE ILE GLU LEU SEQRES 18 A 433 PRO ASP GLY TYR MET ALA ALA LEU LYS ARG LYS CYS GLU SEQRES 19 A 433 ALA ARG GLY MET LEU LEU ILE LEU ASP GLU ALA GLN THR SEQRES 20 A 433 GLY VAL GLY ARG THR GLY THR MET PHE ALA CYS GLN ARG SEQRES 21 A 433 ASP GLY VAL THR PRO ASP ILE LEU THR LEU SER LYS THR SEQRES 22 A 433 LEU GLY ALA GLY LEU PRO LEU ALA ALA ILE VAL THR SER SEQRES 23 A 433 ALA ALA ILE GLU GLU ARG ALA HIS GLU LEU GLY TYR LEU SEQRES 24 A 433 PHE TYR THR THR HIS VAL SER ASP PRO LEU PRO ALA ALA SEQRES 25 A 433 VAL GLY LEU ARG VAL LEU ASP VAL VAL GLN ARG ASP GLY SEQRES 26 A 433 LEU VAL ALA ARG ALA ASN VAL MET GLY ASP ARG LEU ARG SEQRES 27 A 433 ARG GLY LEU LEU ASP LEU MET GLU ARG PHE ASP CYS ILE SEQRES 28 A 433 GLY ASP VAL ARG GLY ARG GLY LEU LEU LEU GLY VAL GLU SEQRES 29 A 433 ILE VAL LYS ASP ARG ARG THR LYS GLU PRO ALA ASP GLY SEQRES 30 A 433 LEU GLY ALA LYS ILE THR ARG GLU CYS MET ASN LEU GLY SEQRES 31 A 433 LEU SER MET ASN ILE VAL GLN LEU PRO GLY MET GLY GLY SEQRES 32 A 433 VAL PHE ARG ILE ALA PRO PRO LEU THR VAL SER GLU ASP SEQRES 33 A 433 GLU ILE ASP LEU GLY LEU SER LEU LEU GLY GLN ALA ILE SEQRES 34 A 433 GLU ARG ALA LEU HET NA A 435 1 HET CA A 436 1 HET PLP A 434 15 HET MES A 437 12 HETNAM NA SODIUM ION HETNAM CA CALCIUM 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 CA CA 2+ FORMUL 4 PLP C8 H10 N O6 P FORMUL 5 MES C6 H13 N O4 S FORMUL 6 HOH *64(H2 O) HELIX 1 1 ASP A 6 LEU A 17 1 12 HELIX 2 2 THR A 49 SER A 54 1 6 HELIX 3 3 HIS A 61 GLY A 73 1 13 HELIX 4 4 SER A 84 THR A 98 1 15 HELIX 5 5 THR A 110 GLY A 127 1 18 HELIX 6 6 THR A 142 SER A 147 1 6 HELIX 7 7 LEU A 186 SER A 200 1 15 HELIX 8 8 GLY A 224 ARG A 236 1 13 HELIX 9 9 ALA A 257 GLY A 262 1 6 HELIX 10 10 SER A 271 ALA A 276 1 6 HELIX 11 11 ALA A 287 LEU A 296 1 10 HELIX 12 12 ASP A 307 ASP A 324 1 18 HELIX 13 13 GLY A 325 PHE A 348 1 24 HELIX 14 14 GLY A 377 LEU A 389 1 13 HELIX 15 15 SER A 414 LEU A 433 1 20 SHEET 1 A 4 ARG A 31 LYS A 33 0 SHEET 2 A 4 PHE A 36 TYR A 38 -1 O TYR A 38 N ARG A 31 SHEET 3 A 4 ALA A 44 ASP A 47 -1 O ILE A 45 N VAL A 37 SHEET 4 A 4 LEU A 391 SER A 392 1 O SER A 392 N LEU A 46 SHEET 1 B 7 LEU A 102 LEU A 108 0 SHEET 2 B 7 ALA A 281 SER A 286 -1 O THR A 285 N ARG A 104 SHEET 3 B 7 ILE A 267 LEU A 270 -1 N LEU A 270 O ALA A 282 SHEET 4 B 7 LEU A 239 ASP A 243 1 N LEU A 242 O THR A 269 SHEET 5 B 7 LEU A 204 ALA A 209 1 N ALA A 209 O ASP A 243 SHEET 6 B 7 GLU A 130 PHE A 134 1 N GLU A 130 O ALA A 205 SHEET 7 B 7 SER A 164 ILE A 167 1 O ILE A 167 N GLY A 133 SHEET 1 C 2 ILE A 212 LEU A 213 0 SHEET 2 C 2 ILE A 219 GLU A 220 -1 O ILE A 219 N LEU A 213 SHEET 1 D 3 ILE A 351 ARG A 357 0 SHEET 2 D 3 LEU A 360 ASP A 368 -1 O LEU A 360 N ARG A 357 SHEET 3 D 3 GLU A 373 PRO A 374 -1 O GLU A 373 N LYS A 367 SHEET 1 E 4 ILE A 351 ARG A 357 0 SHEET 2 E 4 LEU A 360 ASP A 368 -1 O LEU A 360 N ARG A 357 SHEET 3 E 4 GLY A 403 ILE A 407 -1 O ILE A 407 N LEU A 361 SHEET 4 E 4 ILE A 395 GLN A 397 -1 N VAL A 396 O VAL A 404 LINK NZ LYS A 272 C4A PLP A 434 1555 1555 1.28 LINK O LEU A 78 CA CA A 436 1555 1555 2.95 LINK O ALA A 95 NA NA A 435 1555 1555 2.36 LINK O THR A 98 NA NA A 435 1555 1555 2.41 LINK OG1 THR A 98 NA NA A 435 1555 1555 2.88 LINK O PRO A 99 NA NA A 435 1555 1555 2.82 LINK O LEU A 102 NA NA A 435 1555 1555 2.59 LINK O VAL A 305 CA CA A 436 1555 1555 2.60 LINK OD1 ASP A 307 CA CA A 436 1555 1555 3.00 LINK NA NA A 435 O HOH A 500 1555 1555 2.51 LINK CA CA A 436 O HOH A 481 1555 1555 2.92 LINK CA CA A 436 O HOH A 482 1555 1555 3.08 SITE 1 AC1 5 ALA A 95 THR A 98 PRO A 99 LEU A 102 SITE 2 AC1 5 HOH A 500 SITE 1 AC2 7 LEU A 78 SER A 80 THR A 303 VAL A 305 SITE 2 AC2 7 ASP A 307 HOH A 481 HOH A 482 SITE 1 AC3 15 THR A 110 ALA A 112 ASN A 115 TRP A 138 SITE 2 AC3 15 HIS A 139 GLU A 210 ASP A 243 ALA A 245 SITE 3 AC3 15 GLN A 246 LYS A 272 THR A 302 THR A 303 SITE 4 AC3 15 HOH A 478 HOH A 489 HOH A 490 SITE 1 AC4 8 TRP A 138 SER A 215 GLN A 246 LYS A 272 SITE 2 AC4 8 TYR A 301 ARG A 406 HOH A 442 HOH A 479 CRYST1 150.553 150.553 84.703 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 0.006642 0.003835 0.000000 0.00000 SCALE2 0.000000 0.007670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011806 0.00000