HEADER LYASE 09-MAR-20 6M4Y TITLE STRUCTURE OF A R371A MUTANT OF A GROUP II PLP DEPENDENT DECARBOXYLASE TITLE 2 FROM METHANOCALDOCOCCUS JANNASCHII 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 MUTANT, PROTEIN CONFORMATION, KEYWDS 2 LLP, INTERNAL ALDIMINE, TYROSINE, TYROSINE DECARBOXYLASE, STRUCTURE- KEYWDS 3 ACTIVITY RELATIONSHIP, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.MANOJ,S.CHELLAM GAYATHRI REVDAT 3 29-NOV-23 6M4Y 1 REMARK REVDAT 2 16-DEC-20 6M4Y 1 JRNL REVDAT 1 02-DEC-20 6M4Y 0 JRNL AUTH S.C.GAYATHRI,N.MANOJ JRNL TITL CRYSTALLOGRAPHIC SNAPSHOTS OF THE DUNATHAN AND QUINONOID JRNL TITL 2 INTERMEDIATES PROVIDE INSIGHTS INTO THE REACTION MECHANISM JRNL TITL 3 OF GROUP II DECARBOXYLASES. JRNL REF J.MOL.BIOL. V. 432 66692 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 33122004 JRNL DOI 10.1016/J.JMB.2020.10.026 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.CHELLAM 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. V. 208 137 2019 REMARK 1 REFN ESSN 1095-8657 REMARK 1 DOI 10.1016/J.JSB.2019.08.009 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1715 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 2.1600 - 2.1000 1.00 2774 125 0.1779 0.2091 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.11 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 : 0.010 3117 REMARK 3 ANGLE : 0.999 4226 REMARK 3 CHIRALITY : 0.060 477 REMARK 3 PLANARITY : 0.006 535 REMARK 3 DIHEDRAL : 12.710 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 6M4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4-5.6 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 AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : DOUBLE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM V7.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35618 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 26.50 REMARK 200 R MERGE (I) : 0.20800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 25.90 REMARK 200 R MERGE FOR SHELL (I) : 1.20200 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 (%): 61.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 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 60.85000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.22000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.27500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.22000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.22000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.42500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.22000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.22000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.27500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.22000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.22000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.42500 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 60.85000 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: 11390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -136.0 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 584 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 ARG A 2 REMARK 465 THR A 275 REMARK 465 GLU A 276 REMARK 465 THR A 277 REMARK 465 ARG A 278 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 LYS A 20 CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 72 NZ REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 ASP A 85 CG OD1 OD2 REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 GLU A 121 OE1 OE2 REMARK 470 GLU A 153 CD OE1 OE2 REMARK 470 LYS A 160 CE NZ REMARK 470 GLU A 167 CG CD OE1 OE2 REMARK 470 GLU A 182 CD OE1 OE2 REMARK 470 LYS A 194 NZ REMARK 470 LYS A 197 CE NZ REMARK 470 GLU A 198 OE1 REMARK 470 LYS A 220 NZ REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 ASN A 227 CB CG OD1 ND2 REMARK 470 LYS A 229 CE NZ REMARK 470 ARG A 265 NE CZ NH1 NH2 REMARK 470 ASP A 268 CG OD1 OD2 REMARK 470 ASP A 270 CG OD1 OD2 REMARK 470 ALA A 271 CB REMARK 470 LEU A 274 CB CG CD1 CD2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 322 CE NZ REMARK 470 LYS A 323 CD CE NZ REMARK 470 LYS A 330 CG CD CE NZ REMARK 470 GLU A 343 CD OE1 OE2 REMARK 470 GLU A 345 CG CD OE1 OE2 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 CD CE NZ REMARK 470 ARG A 355 NE CZ NH1 NH2 REMARK 470 ASP A 356 OD1 OD2 REMARK 470 VAL A 363 CG1 REMARK 470 ASN A 365 CG OD1 ND2 REMARK 470 CYS A 366 CB SG REMARK 470 VAL A 367 CG2 REMARK 470 LYS A 368 CD CE NZ REMARK 470 LYS A 379 CG CD CE NZ REMARK 470 ARG A 380 NE CZ NH1 NH2 REMARK 470 GLU A 388 CD OE1 OE2 REMARK 470 ILE A 393 CD1 REMARK 470 ARG A 395 CD NE CZ NH1 NH2 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 50.60 -96.75 REMARK 500 VAL A 91 -164.38 -108.61 REMARK 500 PHE A 230 -4.70 -151.08 REMARK 500 ASP A 231 -162.95 -104.21 REMARK 500 LLP A 245 -104.98 -97.01 REMARK 500 LEU A 337 -163.81 -114.52 REMARK 500 ASP A 344 112.60 -171.20 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 SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6JY1 RELATED DB: PDB REMARK 900 THE WILD TYPE PROTEIN REMARK 900 RELATED ID: 6LDR RELATED DB: PDB REMARK 900 THE K245A MUTANT IN COMPLEX WITH PLP REMARK 900 RELATED ID: 6LDS RELATED DB: PDB REMARK 900 THE K245A MUTANT IN COMPLEX WITH PRE-DECARBOXYLATION INTERMEDIATE REMARK 900 RELATED ID: 6LDT RELATED DB: PDB REMARK 900 THE K245A MUTANT IN COMPLEX WITH POST-DECARBOXYLATION INTERMEDIATE DBREF 6M4Y A 1 396 UNP Q60358 MFNA_METJA 1 396 SEQADV 6M4Y MET A -18 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y GLY A -17 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y SER A -16 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y ASP A -15 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y LYS A -14 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y ILE A -13 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y HIS A -12 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y HIS A -11 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y HIS A -10 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y HIS A -9 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y HIS A -8 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y HIS A -7 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y GLU A -6 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y ASN A -5 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y LEU A -4 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y TYR A -3 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y PHE A -2 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y GLN A -1 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y GLY A 0 UNP Q60358 EXPRESSION TAG SEQADV 6M4Y ALA A 371 UNP Q60358 ARG 371 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 LYS 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 LLP 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 ALA 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 6M4Y LLP A 245 LYS MODIFIED RESIDUE HET LLP A 245 37 HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET GOL A 405 9 HET GOL A 406 9 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 SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *283(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 HIS A 132 ASP A 143 1 12 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 ARG A 395 1 17 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 ILE A 241 -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 LYS 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 ILE A 147 N ILE A 125 SHEET 1 AA2 3 ILE A 339 GLU A 343 0 SHEET 2 AA2 3 ALA A 369 VAL A 373 -1 O ILE A 372 N VAL A 340 SHEET 3 AA2 3 SER A 362 VAL A 363 -1 N SER A 362 O ALA A 371 LINK C HIS A 244 N LLP A 245 1555 1555 1.33 LINK C LLP A 245 N MET A 246 1555 1555 1.34 CISPEP 1 ILE A 251 PRO A 252 0 -4.96 SITE 1 AC1 5 ASN A 316 LYS A 379 ARG A 380 HOH A 504 SITE 2 AC1 5 HOH A 615 SITE 1 AC2 5 LYS A 12 ASP A 164 ASP A 168 HOH A 545 SITE 2 AC2 5 HOH A 684 SITE 1 AC3 4 SER A 10 GLU A 11 TYR A 169 TYR A 300 SITE 1 AC4 4 ILE A 333 GLU A 334 HOH A 518 HOH A 640 SITE 1 AC5 7 ASN A 40 VAL A 41 LEU A 42 HIS A 248 SITE 2 AC5 7 ILE A 309 HOH A 578 HOH A 698 SITE 1 AC6 7 LYS A 112 SER A 118 ASN A 120 ASP A 170 SITE 2 AC6 7 VAL A 171 ASP A 172 HOH A 610 CRYST1 98.440 98.440 121.700 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 0.010158 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010158 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008217 0.00000