HEADER LYASE 23-NOV-19 6LDR TITLE STRUCTURE OF A K245A MUTANT OF A GROUP II PLP DEPENDENT DECARBOXYLASE TITLE 2 FROM METHANOCALDOCOCCUS JANNASCHII, IN COMPLEX WITH PLP COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-TYROSINE/L-ASPARTATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TDC/ADC; COMPND 5 EC: 4.1.1.11,4.1.1.25; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII (STRAIN ATCC SOURCE 3 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440); SOURCE 4 ORGANISM_TAXID: 243232; SOURCE 5 STRAIN: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440; SOURCE 6 ATCC: ATCC 43067; SOURCE 7 GENE: MFNA, MJ0050; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: B; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PSPEEDET KEYWDS PLP DEPENDENT DECARBOXYLASE, CATALYTIC DOMAIN, PROTEIN CONFORMATION, KEYWDS 2 PYRIDOXAL 5-PHOSPHATE, LYS MUTANT, GROUP II DECARBOXYLASE, KEYWDS 3 STRUCTURE-ACTIVITY RELATIONSHIP, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.MANOJ,S.C.GAYATHRI REVDAT 3 22-NOV-23 6LDR 1 REMARK REVDAT 2 16-DEC-20 6LDR 1 JRNL REVDAT 1 02-DEC-20 6LDR 0 JRNL AUTH S.CHELLAM GAYATHRI,N.MANOJ JRNL TITL STRUCTURAL INSIGHTS INTO THE MECHANISM OF INTERNAL ALDIMINE JRNL TITL 2 FORMATION AND CATALYTIC LOOP DYNAMICS IN AN ARCHAEAL GROUP JRNL TITL 3 II DECARBOXYLASE. JRNL REF J.STRUCT.BIOL. V. 208 137 2019 JRNL REFN ESSN 1095-8657 JRNL PMID 31445086 JRNL DOI 10.1016/J.JSB.2019.08.009 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.C.GAYATHRI,N.MANOJ REMARK 1 TITL STRUCTURAL INSIGHTS INTO THE MECHANISM OF INTERNAL ALDIMINE REMARK 1 TITL 2 FORMATION AND CATALYTIC LOOP DYNAMICS IN AN ARCHAEAL GROUP REMARK 1 TITL 3 II DECARBOXYLASE. REMARK 1 REF J. STRUCT. BIOL. 2019 REMARK 1 REFN ESSN 1095-8657 REMARK 1 DOI 10.1016/J.JSB.2019.08.009 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 56865 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.8200 - 4.8600 1.00 2950 144 0.2082 0.2289 REMARK 3 2 4.8600 - 3.8600 1.00 2784 147 0.1366 0.1603 REMARK 3 3 3.8600 - 3.3700 1.00 2763 149 0.1491 0.1975 REMARK 3 4 3.3700 - 3.0600 1.00 2725 138 0.1681 0.1920 REMARK 3 5 3.0600 - 2.8400 1.00 2706 147 0.1717 0.2152 REMARK 3 6 2.8400 - 2.6700 1.00 2720 129 0.1642 0.1837 REMARK 3 7 2.6700 - 2.5400 1.00 2703 135 0.1612 0.1749 REMARK 3 8 2.5400 - 2.4300 1.00 2689 147 0.1551 0.1948 REMARK 3 9 2.4300 - 2.3400 1.00 2666 148 0.1571 0.1884 REMARK 3 10 2.3400 - 2.2600 1.00 2700 134 0.1580 0.1910 REMARK 3 11 2.2600 - 2.1800 1.00 2674 129 0.1580 0.1722 REMARK 3 12 2.1800 - 2.1200 1.00 2710 132 0.1583 0.1592 REMARK 3 13 2.1200 - 2.0700 1.00 2674 123 0.1668 0.1761 REMARK 3 14 2.0700 - 2.0200 1.00 2660 139 0.1658 0.1790 REMARK 3 15 2.0200 - 1.9700 1.00 2655 155 0.1790 0.2096 REMARK 3 16 1.9700 - 1.9300 1.00 2654 141 0.1945 0.2475 REMARK 3 17 1.9300 - 1.8900 1.00 2661 139 0.2170 0.2790 REMARK 3 18 1.8900 - 1.8500 1.00 2644 154 0.2157 0.2424 REMARK 3 19 1.8500 - 1.8200 1.00 2634 147 0.2295 0.2750 REMARK 3 20 1.8200 - 1.7900 1.00 2677 139 0.2377 0.2452 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 3120 REMARK 3 ANGLE : 0.992 4234 REMARK 3 CHIRALITY : 0.061 473 REMARK 3 PLANARITY : 7.000 539 REMARK 3 DIHEDRAL : 14.092 1859 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300013714. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : S1 (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM V7.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56951 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 49.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 1.11900 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: PHENIX REMARK 200 STARTING MODEL: 6JY1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH 5.4, 0.2M REMARK 280 SODIUM POTASSIUM TARTARATE, 2.0M AMMONIUM SULPHATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 60.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.19000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.35000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.19000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.19000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.45000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.19000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.19000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.35000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.19000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.19000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.45000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 60.90000 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: 11240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 533 LIES ON A SPECIAL POSITION. 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 -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 ASP A -15 REMARK 465 LYS A -14 REMARK 465 ILE A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ASP A 270 REMARK 465 ALA A 271 REMARK 465 PRO A 272 REMARK 465 TYR A 273 REMARK 465 LEU A 274 REMARK 465 THR A 275 REMARK 465 GLU A 276 REMARK 465 THR A 277 REMARK 465 ARG A 278 REMARK 465 CYS A 364 REMARK 465 ASN A 365 REMARK 465 CYS A 366 REMARK 465 ARG A 395 REMARK 465 ASP A 396 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 ARG A 2 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 7 CE NZ REMARK 470 LYS A 20 CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 LYS A 115 NZ REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 GLU A 121 CD OE1 OE2 REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 GLU A 167 OE1 OE2 REMARK 470 LYS A 194 CE NZ REMARK 470 LYS A 197 CE NZ REMARK 470 ASP A 219 CG OD1 OD2 REMARK 470 LYS A 220 NZ REMARK 470 LYS A 223 CE NZ REMARK 470 LYS A 224 CD CE NZ REMARK 470 LYS A 229 NZ REMARK 470 LYS A 264 NZ REMARK 470 ARG A 265 NE CZ NH1 NH2 REMARK 470 GLU A 304 CG CD OE1 OE2 REMARK 470 LYS A 308 CD CE NZ REMARK 470 LYS A 322 CD CE NZ REMARK 470 LYS A 323 CD CE NZ REMARK 470 LYS A 325 CE NZ REMARK 470 ASN A 328 CG OD1 ND2 REMARK 470 LYS A 330 CG CD CE NZ REMARK 470 GLU A 334 CD OE1 OE2 REMARK 470 GLU A 345 CG CD OE1 OE2 REMARK 470 ASP A 346 CG OD1 OD2 REMARK 470 LYS A 348 CD CE NZ REMARK 470 GLU A 349 CG CD OE1 OE2 REMARK 470 LYS A 352 CG CD CE NZ REMARK 470 LYS A 353 NZ REMARK 470 ARG A 355 NE CZ NH1 NH2 REMARK 470 ARG A 357 CZ NH1 NH2 REMARK 470 VAL A 367 CB CG1 CG2 REMARK 470 LYS A 368 CG CD CE NZ REMARK 470 ARG A 380 CZ NH1 NH2 REMARK 470 GLU A 388 CD OE1 OE2 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 GLU A 54 53.33 -97.68 REMARK 500 VAL A 91 -160.89 -106.03 REMARK 500 PHE A 230 -3.80 -148.84 REMARK 500 ASP A 231 -161.28 -104.30 REMARK 500 ALA A 245 -101.19 -90.81 REMARK 500 LEU A 337 -165.98 -113.00 REMARK 500 ASP A 346 40.37 -88.07 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 825 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 826 DISTANCE = 6.56 ANGSTROMS 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6JY1 RELATED DB: PDB REMARK 900 6JY1 CONTAINS THE WILD TYPE PROTEIN COVALENTLY BOUND TO PLP (LLP) REMARK 900 IN THE ACTIVE SITE DBREF 6LDR A 1 396 UNP Q60358 MFNA_METJA 1 396 SEQADV 6LDR MET A -18 UNP Q60358 EXPRESSION TAG SEQADV 6LDR GLY A -17 UNP Q60358 EXPRESSION TAG SEQADV 6LDR SER A -16 UNP Q60358 EXPRESSION TAG SEQADV 6LDR ASP A -15 UNP Q60358 EXPRESSION TAG SEQADV 6LDR LYS A -14 UNP Q60358 EXPRESSION TAG SEQADV 6LDR ILE A -13 UNP Q60358 EXPRESSION TAG SEQADV 6LDR HIS A -12 UNP Q60358 EXPRESSION TAG SEQADV 6LDR HIS A -11 UNP Q60358 EXPRESSION TAG SEQADV 6LDR HIS A -10 UNP Q60358 EXPRESSION TAG SEQADV 6LDR HIS A -9 UNP Q60358 EXPRESSION TAG SEQADV 6LDR HIS A -8 UNP Q60358 EXPRESSION TAG SEQADV 6LDR HIS A -7 UNP Q60358 EXPRESSION TAG SEQADV 6LDR GLU A -6 UNP Q60358 EXPRESSION TAG SEQADV 6LDR ASN A -5 UNP Q60358 EXPRESSION TAG SEQADV 6LDR LEU A -4 UNP Q60358 EXPRESSION TAG SEQADV 6LDR TYR A -3 UNP Q60358 EXPRESSION TAG SEQADV 6LDR PHE A -2 UNP Q60358 EXPRESSION TAG SEQADV 6LDR GLN A -1 UNP Q60358 EXPRESSION TAG SEQADV 6LDR GLY A 0 UNP Q60358 EXPRESSION TAG SEQADV 6LDR ALA A 245 UNP Q60358 LYS 245 ENGINEERED MUTATION SEQRES 1 A 415 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS GLU SEQRES 2 A 415 ASN LEU TYR PHE GLN GLY MET ARG ASN MET GLN GLU LYS SEQRES 3 A 415 GLY VAL SER GLU LYS GLU ILE LEU GLU GLU LEU LYS LYS SEQRES 4 A 415 TYR ARG SER LEU ASP LEU LYS TYR GLU ASP GLY ASN ILE SEQRES 5 A 415 PHE GLY SER MET CYS SER ASN VAL LEU PRO ILE THR ARG SEQRES 6 A 415 LYS ILE VAL ASP ILE PHE LEU GLU THR ASN LEU GLY ASP SEQRES 7 A 415 PRO GLY LEU PHE LYS GLY THR LYS LEU LEU GLU GLU LYS SEQRES 8 A 415 ALA VAL ALA LEU LEU GLY SER LEU LEU ASN ASN LYS ASP SEQRES 9 A 415 ALA TYR GLY HIS ILE VAL SER GLY GLY THR GLU ALA ASN SEQRES 10 A 415 LEU MET ALA LEU ARG CYS ILE LYS ASN ILE TRP ARG GLU SEQRES 11 A 415 LYS ARG ARG LYS GLY LEU SER LYS ASN GLU HIS PRO LLP SEQRES 12 A 415 ILE ILE VAL PRO ILE THR ALA HIS PHE SER PHE GLU LYS SEQRES 13 A 415 GLY ARG GLU MET MET ASP LEU GLU TYR ILE TYR ALA PRO SEQRES 14 A 415 ILE LYS GLU ASP TYR THR ILE ASP GLU LYS PHE VAL LYS SEQRES 15 A 415 ASP ALA VAL GLU ASP TYR ASP VAL ASP GLY ILE ILE GLY SEQRES 16 A 415 ILE ALA GLY THR THR GLU LEU GLY THR ILE ASP ASN ILE SEQRES 17 A 415 GLU GLU LEU SER LYS ILE ALA LYS GLU ASN ASN ILE TYR SEQRES 18 A 415 ILE HIS VAL ASP ALA ALA PHE GLY GLY LEU VAL ILE PRO SEQRES 19 A 415 PHE LEU ASP ASP LYS TYR LYS LYS LYS GLY VAL ASN TYR SEQRES 20 A 415 LYS PHE ASP PHE SER LEU GLY VAL ASP SER ILE THR ILE SEQRES 21 A 415 ASP PRO HIS ALA MET GLY HIS CYS PRO ILE PRO SER GLY SEQRES 22 A 415 GLY ILE LEU PHE LYS ASP ILE GLY TYR LYS ARG TYR LEU SEQRES 23 A 415 ASP VAL ASP ALA PRO TYR LEU THR GLU THR ARG GLN ALA SEQRES 24 A 415 THR ILE LEU GLY THR ARG VAL GLY PHE GLY GLY ALA CYS SEQRES 25 A 415 THR TYR ALA VAL LEU ARG TYR LEU GLY ARG GLU GLY GLN SEQRES 26 A 415 ARG LYS ILE VAL ASN GLU CYS MET GLU ASN THR LEU TYR SEQRES 27 A 415 LEU TYR LYS LYS LEU LYS GLU ASN ASN PHE LYS PRO VAL SEQRES 28 A 415 ILE GLU PRO ILE LEU ASN ILE VAL ALA ILE GLU ASP GLU SEQRES 29 A 415 ASP TYR LYS GLU VAL CYS LYS LYS LEU ARG ASP ARG GLY SEQRES 30 A 415 ILE TYR VAL SER VAL CYS ASN CYS VAL LYS ALA LEU ARG SEQRES 31 A 415 ILE VAL VAL MET PRO HIS ILE LYS ARG GLU HIS ILE ASP SEQRES 32 A 415 ASN PHE ILE GLU ILE LEU ASN SER ILE LYS ARG ASP MODRES 6LDR LLP A 124 LYS MODIFIED RESIDUE HET LLP A 124 37 HET PLP A 401 48 HET NH4 A 402 5 HET GOL A 403 9 HET GOL A 404 9 HET SO4 A 405 5 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM NH4 AMMONIUM ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 NH4 H4 N 1+ FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *326(H2 O) HELIX 1 AA1 SER A 10 ASP A 25 1 16 HELIX 2 AA2 LYS A 27 GLY A 31 5 5 HELIX 3 AA3 PRO A 43 LEU A 53 1 11 HELIX 4 AA4 ASP A 59 LEU A 62 5 4 HELIX 5 AA5 PHE A 63 LEU A 81 1 19 HELIX 6 AA6 GLY A 93 LYS A 115 1 23 HELIX 7 AA7 PHE A 133 ASP A 143 1 11 HELIX 8 AA8 ASP A 158 TYR A 169 1 12 HELIX 9 AA9 ASN A 188 ASN A 200 1 13 HELIX 10 AB1 PHE A 209 LEU A 217 5 9 HELIX 11 AB2 ASP A 218 LYS A 222 5 5 HELIX 12 AB3 ASP A 231 GLY A 235 5 5 HELIX 13 AB4 ASP A 260 ASP A 268 5 9 HELIX 14 AB5 GLY A 288 ASN A 327 1 40 HELIX 15 AB6 ASP A 346 ARG A 357 1 12 HELIX 16 AB7 LYS A 379 LYS A 394 1 16 SHEET 1 AA1 7 TYR A 87 VAL A 91 0 SHEET 2 AA1 7 GLY A 254 PHE A 258 -1 O PHE A 258 N TYR A 87 SHEET 3 AA1 7 SER A 238 THR A 240 -1 N ILE A 239 O LEU A 257 SHEET 4 AA1 7 TYR A 202 ASP A 206 1 N VAL A 205 O SER A 238 SHEET 5 AA1 7 GLY A 173 ILE A 177 1 N GLY A 176 O ASP A 206 SHEET 6 AA1 7 LLP A 124 PRO A 128 1 N ILE A 126 O GLY A 173 SHEET 7 AA1 7 GLU A 145 ALA A 149 1 O GLU A 145 N ILE A 125 SHEET 1 AA2 2 ILE A 339 GLU A 343 0 SHEET 2 AA2 2 ALA A 369 VAL A 373 -1 O ILE A 372 N VAL A 340 LINK C PRO A 123 N LLP A 124 1555 1555 1.34 LINK C LLP A 124 N ILE A 125 1555 1555 1.33 CISPEP 1 ILE A 251 PRO A 252 0 1.21 SITE 1 AC1 16 MET A 37 GLY A 93 GLY A 94 THR A 95 SITE 2 AC1 16 ASN A 98 HIS A 132 THR A 181 ASP A 206 SITE 3 AC1 16 ALA A 208 ASP A 242 HIS A 244 THR A 285 SITE 4 AC1 16 HOH A 506 HOH A 511 HOH A 522 HOH A 682 SITE 1 AC2 4 SER A 36 ASN A 56 ASP A 59 HOH A 647 SITE 1 AC3 3 ASP A 260 GLY A 262 TYR A 263 SITE 1 AC4 7 LYS A 112 LEU A 117 SER A 118 ASN A 120 SITE 2 AC4 7 ASP A 170 VAL A 171 ASP A 172 SITE 1 AC5 5 ASN A 316 LYS A 379 ARG A 380 HOH A 501 SITE 2 AC5 5 HOH A 505 CRYST1 98.380 98.380 121.800 90.00 90.00 90.00 P 43 21 2 8 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 0.010165 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008210 0.00000