HEADER FLAVOPROTEIN 23-MAY-23 8P4W TITLE LACTOBACILLUS PLANTARUM LPDD MUTANT - H35A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN LPDD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GALLATE DECARBOXYLASE SUBUNIT D; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTIPLANTIBACILLUS PLANTARUM; SOURCE 3 ORGANISM_TAXID: 1590; SOURCE 4 GENE: LPDD, LP_0272; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 6 PPPARG4; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS UBID, UBIX, LPDD, FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.GAHLOTH,D.LEYS REVDAT 1 12-JUN-24 8P4W 0 JRNL AUTH D.GAHLOTH,D.LEYS JRNL TITL GALLATE DECARBOXYLASE SUBUNIT D, LPDD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 663 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 48.1460 - 3.0436 1.00 2964 140 0.1759 0.2019 REMARK 3 2 3.0436 - 2.4158 1.00 2793 138 0.2003 0.2282 REMARK 3 3 2.4158 - 2.1104 1.00 2780 115 0.1964 0.2200 REMARK 3 4 2.1104 - 1.9174 1.00 2748 141 0.2198 0.2318 REMARK 3 5 1.9174 - 1.7800 0.98 2670 129 0.2800 0.3273 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.940 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 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 : 0.006 936 REMARK 3 ANGLE : 0.749 1274 REMARK 3 CHIRALITY : 0.052 152 REMARK 3 PLANARITY : 0.006 162 REMARK 3 DIHEDRAL : 2.564 558 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 8P4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15850 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 48.146 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH 4.6, 2.0M REMARK 280 AMMONIUM SULPHATE, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 41.69000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.48500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.48500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.84500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.48500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.48500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.53500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.48500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.48500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.84500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.48500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.48500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 62.53500 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 41.69000 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: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 -41.69000 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 330 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 438 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 VAL A 121 REMARK 465 GLN A 122 REMARK 465 ALA A 123 REMARK 465 GLU A 124 REMARK 465 LYS A 125 REMARK 465 PRO A 126 REMARK 465 GLU A 127 REMARK 465 TYR A 128 REMARK 465 TYR A 129 REMARK 465 GLY A 130 REMARK 465 GLN A 131 REMARK 465 ASP A 132 REMARK 465 GLU A 133 REMARK 465 GLN A 134 REMARK 465 PRO A 135 REMARK 465 ARG A 136 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 HIS A 35 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 419 O HOH A 436 1.99 REMARK 500 O HOH A 401 O HOH A 427 2.06 REMARK 500 NE2 GLN A 97 O HOH A 301 2.07 REMARK 500 O HOH A 371 O HOH A 422 2.15 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 445 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 446 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 447 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A 448 DISTANCE = 6.63 ANGSTROMS DBREF 8P4W A 1 136 UNP F9UT68 LPDD_LACPL 1 136 SEQRES 1 A 136 MET ALA THR PHE THR THR GLU GLN ALA GLY TYR GLN MET SEQRES 2 A 136 GLN ALA ILE LEU GLN VAL ILE GLY TYR ASP LEU LEU ILE SEQRES 3 A 136 VAL VAL THR GLY GLY THR ASN PRO HIS ILE GLY ASP VAL SEQRES 4 A 136 THR THR LEU THR ALA SER THR VAL PRO GLU THR VAL LYS SEQRES 5 A 136 PHE PRO SER HIS ASP GLY ARG PHE HIS LYS ASP ASN PHE SEQRES 6 A 136 ILE SER GLU ARG MET ALA LYS ARG ILE GLN ARG TYR LEU SEQRES 7 A 136 ALA GLY SER CYS THR ILE THR ALA GLY ILE HIS VAL ASN SEQRES 8 A 136 GLN ILE THR LYS ALA GLN ILE ALA ALA ALA ALA PRO MET SEQRES 9 A 136 THR ASP ASP LEU SER ARG GLN ILE ILE SER TRP LEU GLN SEQRES 10 A 136 ALA HIS PRO VAL GLN ALA GLU LYS PRO GLU TYR TYR GLY SEQRES 11 A 136 GLN ASP GLU GLN PRO ARG HET PO4 A 201 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *148(H2 O) HELIX 1 AA1 ASP A 63 GLN A 75 1 13 HELIX 2 AA2 ARG A 76 LEU A 78 5 3 HELIX 3 AA3 THR A 94 HIS A 119 1 26 SHEET 1 AA1 6 ALA A 2 GLN A 8 0 SHEET 2 AA1 6 TYR A 11 ILE A 20 -1 O LEU A 17 N ALA A 2 SHEET 3 AA1 6 ASP A 23 GLY A 30 -1 O ASP A 23 N ILE A 20 SHEET 4 AA1 6 SER A 81 GLY A 87 1 O THR A 85 N ILE A 26 SHEET 5 AA1 6 ASP A 38 THR A 43 -1 N THR A 40 O ILE A 84 SHEET 6 AA1 6 THR A 46 LYS A 52 -1 O GLU A 49 N THR A 41 CRYST1 58.970 58.970 83.380 90.00 90.00 90.00 P 41 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 0.016958 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011993 0.00000