HEADER LYASE 01-FEB-08 3C5Q TITLE CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE (I148L MUTANT) FROM TITLE 2 HELICOBACTER PYLORI COMPLEXED WITH L-LYSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.1.20; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 STRAIN: SS1; SOURCE 4 GENE: LYSA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS DIAMINOPIMELATE DECARBOXYLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HU,D.WU,H.JIANG,X.SHEN REVDAT 4 13-MAR-24 3C5Q 1 REMARK LINK REVDAT 3 13-JUL-11 3C5Q 1 VERSN REVDAT 2 24-FEB-09 3C5Q 1 VERSN REVDAT 1 27-MAY-08 3C5Q 0 JRNL AUTH T.HU,D.WU,J.DING,H.JIANG,X.SHEN JRNL TITL CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE FROM JRNL TITL 2 HELICOBACTER PYLORI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 19222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 984 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 : 3102 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90400 REMARK 3 B22 (A**2) : 0.90400 REMARK 3 B33 (A**2) : -1.80800 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) : 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) : 1.304 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) : 1.243 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.032 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.055 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.934 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 40.90 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NEW_PLP.PARAM REMARK 3 PARAMETER FILE 4 : GOL.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3C5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046374. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19223 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 7.330 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.45 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BICINE, 1.6M AMMONIUM SULFATE, PH REMARK 280 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.88067 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 44.94033 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.94033 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 89.88067 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 44.94033 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PHE A 2 REMARK 465 ALA A 281 REMARK 465 GLN A 282 REMARK 465 LYS A 315 REMARK 465 GLY A 316 REMARK 465 ARG A 317 REMARK 465 HIS A 380 REMARK 465 LYS A 403 REMARK 465 GLY A 404 REMARK 465 VAL A 405 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 PHE A 34 70.06 -118.46 REMARK 500 ASN A 48 112.16 -175.01 REMARK 500 LYS A 143 72.42 53.94 REMARK 500 CYS A 322 144.84 -174.30 REMARK 500 CYS A 329 -5.96 -54.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QGH RELATED DB: PDB REMARK 900 WILDTYPE REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY REMARK 999 EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. DBREF 3C5Q A -19 405 PDB 3C5Q 3C5Q -19 405 SEQRES 1 A 425 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 425 LEU VAL PRO ARG GLY SER HIS MET PHE ASN TYR GLU GLU SEQRES 3 A 425 LEU PHE GLN THR HIS LYS THR PRO PHE TYR LEU TYR ASP SEQRES 4 A 425 PHE ASP LYS ILE LYS GLN ALA PHE LEU ASN TYR LYS GLU SEQRES 5 A 425 ALA PHE LYS GLY ARG LYS SER LEU ILE CYS TYR ALA LEU SEQRES 6 A 425 LYS ALA ASN SER ASN LEU SER ILE LEU SER LEU LEU ALA SEQRES 7 A 425 HIS LEU GLU SER GLY ALA ASP CYS VAL SER ILE GLY GLU SEQRES 8 A 425 ILE GLN ARG ALA LEU LYS ALA GLY ILE LYS PRO TYR ARG SEQRES 9 A 425 ILE VAL PHE SER GLY VAL GLY LYS SER ALA PHE GLU ILE SEQRES 10 A 425 GLU GLN ALA LEU LYS LEU ASN ILE LEU PHE LEU ASN VAL SEQRES 11 A 425 GLU SER PHE MET GLU LEU LYS THR ILE GLU THR ILE ALA SEQRES 12 A 425 GLN SER LEU GLY ILE LYS ALA ARG ILE SER ILE ARG ILE SEQRES 13 A 425 ASN PRO ASN ILE ASP ALA LYS THR HIS PRO TYR LEU SER SEQRES 14 A 425 THR GLY LEU LYS GLU ASN LYS PHE GLY VAL GLY GLU LYS SEQRES 15 A 425 GLU ALA LEU GLU MET PHE LEU TRP ALA LYS LYS SER ALA SEQRES 16 A 425 PHE LEU GLU PRO VAL SER VAL HIS PHE HIS ILE GLY SER SEQRES 17 A 425 GLN LEU LEU ASP LEU GLU PRO ILE ILE GLU ALA SER GLN SEQRES 18 A 425 LYS VAL ALA LYS ILE ALA LYS SER LEU ILE ALA LEU GLY SEQRES 19 A 425 ILE ASP LEU ARG PHE PHE ASP VAL GLY GLY GLY ILE GLY SEQRES 20 A 425 VAL SER TYR GLU ASN GLU GLU THR ILE LYS LEU TYR ASP SEQRES 21 A 425 TYR ALA GLN GLY ILE LEU ASN ALA LEU GLN GLY LEU ASP SEQRES 22 A 425 LEU THR ILE ILE CYS GLU PRO GLY ARG SER ILE VAL ALA SEQRES 23 A 425 GLU SER GLY GLU LEU ILE THR GLN VAL LEU TYR GLU LYS SEQRES 24 A 425 LYS ALA GLN ASN LYS ARG PHE VAL ILE VAL ASP ALA GLY SEQRES 25 A 425 MET ASN ASP PHE LEU ARG PRO SER LEU TYR HIS ALA LYS SEQRES 26 A 425 HIS ALA ILE ARG VAL ILE THR PRO SER LYS GLY ARG GLU SEQRES 27 A 425 ILE SER PRO CYS ASP VAL VAL GLY PRO VAL CYS GLU SER SEQRES 28 A 425 SER ASP THR PHE LEU LYS ASP ALA HIS LEU PRO GLU LEU SEQRES 29 A 425 GLU PRO GLY ASP LYS ILE ALA ILE GLU LYS VAL GLY ALA SEQRES 30 A 425 TYR GLY SER SER MET ALA SER GLN TYR ASN SER ARG PRO SEQRES 31 A 425 LYS LEU LEU GLU LEU ALA LEU GLU ASP HIS LYS ILE ARG SEQRES 32 A 425 VAL ILE ARG LYS ARG GLU ALA LEU GLU ASP LEU TRP ARG SEQRES 33 A 425 LEU GLU GLU GLU GLY LEU LYS GLY VAL HET PLP A 406 15 HET LYS A 407 10 HET GOL A1003 6 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM LYS LYSINE HETNAM GOL GLYCEROL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 LYS C6 H15 N2 O2 1+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *121(H2 O) HELIX 1 1 ASN A 3 HIS A 11 1 9 HELIX 2 2 PHE A 20 PHE A 34 1 15 HELIX 3 3 LYS A 46 ASN A 48 5 3 HELIX 4 4 ASN A 50 LEU A 60 1 11 HELIX 5 5 SER A 68 GLY A 79 1 12 HELIX 6 6 LYS A 81 TYR A 83 5 3 HELIX 7 7 SER A 93 LEU A 103 1 11 HELIX 8 8 SER A 112 GLY A 127 1 16 HELIX 9 9 HIS A 145 SER A 149 5 5 HELIX 10 10 GLY A 160 SER A 174 1 15 HELIX 11 11 LEU A 193 LEU A 213 1 21 HELIX 12 12 LYS A 237 LEU A 249 1 13 HELIX 13 13 GLY A 261 ALA A 266 1 6 HELIX 14 14 LEU A 297 HIS A 303 1 7 HELIX 15 15 GLY A 359 ALA A 363 5 5 HELIX 16 16 ALA A 390 ARG A 396 1 7 HELIX 17 17 LEU A 397 GLU A 399 5 3 SHEET 1 A 6 ILE A 308 VAL A 310 0 SHEET 2 A 6 LYS A 349 ILE A 352 -1 O ALA A 351 N ARG A 309 SHEET 3 A 6 GLY A 269 LYS A 279 -1 N LEU A 271 O ILE A 352 SHEET 4 A 6 PHE A 286 VAL A 289 -1 O PHE A 286 N LYS A 279 SHEET 5 A 6 ILE A 319 VAL A 325 1 O VAL A 325 N VAL A 289 SHEET 6 A 6 THR A 334 PRO A 342 -1 O ALA A 339 N CYS A 322 SHEET 1 B 6 ILE A 308 VAL A 310 0 SHEET 2 B 6 LYS A 349 ILE A 352 -1 O ALA A 351 N ARG A 309 SHEET 3 B 6 GLY A 269 LYS A 279 -1 N LEU A 271 O ILE A 352 SHEET 4 B 6 PHE A 15 ASP A 19 -1 N PHE A 15 O ILE A 272 SHEET 5 B 6 LEU A 373 LEU A 377 1 O LEU A 375 N TYR A 16 SHEET 6 B 6 ILE A 382 ARG A 386 -1 O ARG A 383 N ALA A 376 SHEET 1 C 9 SER A 39 ALA A 44 0 SHEET 2 C 9 GLY A 63 CYS A 66 1 O GLY A 63 N ILE A 41 SHEET 3 C 9 ILE A 85 PHE A 87 1 O VAL A 86 N CYS A 66 SHEET 4 C 9 PHE A 107 VAL A 110 1 O ASN A 109 N PHE A 87 SHEET 5 C 9 ALA A 130 ARG A 135 1 O SER A 133 N LEU A 108 SHEET 6 C 9 LEU A 177 HIS A 183 1 O GLU A 178 N ALA A 130 SHEET 7 C 9 PHE A 219 ASP A 221 1 O ASP A 221 N VAL A 182 SHEET 8 C 9 THR A 255 CYS A 258 1 O THR A 255 N PHE A 220 SHEET 9 C 9 SER A 39 ALA A 44 1 N CYS A 42 O CYS A 258 LINK C4A PLP A 406 NZ LYS A 407 1555 1555 1.28 CISPEP 1 THR A 13 PRO A 14 0 -0.07 SITE 1 AC1 15 ALA A 44 ASP A 65 HIS A 185 SER A 188 SITE 2 AC1 15 GLY A 225 GLU A 259 PRO A 260 GLY A 261 SITE 3 AC1 15 ARG A 262 TYR A 358 LYS A 407 HOH A1004 SITE 4 AC1 15 HOH A1011 HOH A1015 HOH A1120 SITE 1 AC2 8 LEU A 148 ARG A 262 ARG A 298 TYR A 302 SITE 2 AC2 8 GLU A 330 TYR A 358 MET A 362 TYR A 366 SITE 1 AC3 5 LEU A 101 ASN A 104 ILE A 105 LEU A 108 SITE 2 AC3 5 ARG A 131 CRYST1 79.111 79.111 134.821 90.00 90.00 120.00 P 32 2 1 6 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 0.012640 0.007298 0.000000 0.00000 SCALE2 0.000000 0.014596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007417 0.00000