HEADER OXIDOREDUCTASE 10-JUL-14 4QUK TITLE CRYSTAL STRUCTURE OF CINNAMYL-ALCOHOL DEHYDROGENASE 2 MUTANT K169A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFLAVONOL-4-REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CINNAMYL ALCOHOL DEHYDROGENASE 2; COMPND 5 EC: 1.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MEDICAGO TRUNCATULA; SOURCE 3 ORGANISM_COMMON: BARREL MEDIC; SOURCE 4 ORGANISM_TAXID: 3880; SOURCE 5 GENE: MTR_3G005170; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS DEHYDROGENASE, MONOLIGNOL, MUTANT, SHORT-CHAIN KEYWDS 2 DEHYDROGENASE/REDUCTASE, ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.PAN,X.WANG REVDAT 3 20-SEP-23 4QUK 1 SEQADV REVDAT 2 12-NOV-14 4QUK 1 JRNL REVDAT 1 01-OCT-14 4QUK 0 JRNL AUTH H.PAN,R.ZHOU,G.V.LOUIE,J.K.MUHLEMANN,E.K.BOMATI,M.E.BOWMAN, JRNL AUTH 2 N.DUDAREVA,R.A.DIXON,J.P.NOEL,X.WANG JRNL TITL STRUCTURAL STUDIES OF CINNAMOYL-COA REDUCTASE AND JRNL TITL 2 CINNAMYL-ALCOHOL DEHYDROGENASE, KEY ENZYMES OF MONOLIGNOL JRNL TITL 3 BIOSYNTHESIS. JRNL REF PLANT CELL V. 26 3709 2014 JRNL REFN ISSN 1040-4651 JRNL PMID 25217505 JRNL DOI 10.1105/TPC.114.127399 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 221965.150 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 24520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2433 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3340 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 351 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2419 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : 1.36000 REMARK 3 B33 (A**2) : -0.72000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.03 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 61.29 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4QUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 93 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 : RIGAKU RUH3R 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24741 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 28.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 4QTZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1 M BIS-TRIS, PH 6.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 18.89850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.02250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.28250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.02250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.89850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.28250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 88 REMARK 465 PRO A 89 REMARK 465 PHE A 90 REMARK 465 TYR A 91 REMARK 465 HIS A 92 REMARK 465 ASP A 93 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 LYS A 95 -72.35 -100.12 REMARK 500 LEU A 101 -68.59 -137.42 REMARK 500 SER A 129 -141.85 -114.19 REMARK 500 TYR A 136 71.56 -101.42 REMARK 500 ALA A 193 -133.99 -101.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QTZ RELATED DB: PDB REMARK 900 CINNAMYL-ALCOHOL DEHYDROGENASE DBREF 4QUK A 8 326 UNP G7IYC1 G7IYC1_MEDTR 8 326 SEQADV 4QUK ALA A 169 UNP G7IYC1 LYS 169 ENGINEERED MUTATION SEQRES 1 A 319 ASN VAL VAL CYS VAL THR GLY ALA SER GLY TYR ILE ALA SEQRES 2 A 319 SER TRP LEU VAL ARG LEU LEU LEU HIS ARG GLY TYR THR SEQRES 3 A 319 VAL LYS ALA THR VAL ARG ASP PRO ASN ASP PRO LYS LYS SEQRES 4 A 319 VAL ASP HIS LEU VAL LYS LEU ASP GLY ALA LYS GLU ARG SEQRES 5 A 319 LEU GLN LEU PHE LYS ALA ASN LEU LEU GLU GLU GLY ALA SEQRES 6 A 319 PHE ASP SER VAL VAL GLN GLY CYS HIS GLY VAL PHE HIS SEQRES 7 A 319 THR ALA SER PRO PHE TYR HIS ASP VAL LYS ASP PRO GLN SEQRES 8 A 319 ALA GLU LEU ILE ASP PRO ALA LEU LYS GLY THR LEU ASN SEQRES 9 A 319 VAL LEU ASN SER CYS ALA LYS SER PRO SER LEU LYS ARG SEQRES 10 A 319 VAL VAL LEU THR SER SER ILE ALA ALA VAL ALA TYR ASN SEQRES 11 A 319 GLY LYS PRO ARG THR PRO ASP VAL VAL VAL ASP GLU THR SEQRES 12 A 319 TRP PHE THR ASP ALA ASP PHE CYS ALA LYS SER ASN LEU SEQRES 13 A 319 TRP TYR VAL VAL SER ALA THR LEU ALA GLU GLU ALA ALA SEQRES 14 A 319 TRP LYS PHE VAL LYS GLU ASN ASN ILE ASP MET VAL THR SEQRES 15 A 319 ILE ASN PRO ALA MET VAL ILE GLY PRO LEU LEU GLN PRO SEQRES 16 A 319 VAL LEU ASN THR SER ALA ALA ALA ILE LEU ASN LEU ILE SEQRES 17 A 319 ASN GLY ALA GLN THR PHE PRO ASN ALA SER PHE GLY TRP SEQRES 18 A 319 VAL ASN VAL LYS ASP VAL ALA ASN ALA HIS ILE LEU ALA SEQRES 19 A 319 TYR GLU ASN ALA SER ALA SER GLY ARG HIS CYS LEU VAL SEQRES 20 A 319 GLU ARG VAL ALA HIS TYR SER GLU VAL VAL ARG ILE LEU SEQRES 21 A 319 ARG GLU LEU TYR PRO SER LEU GLN LEU PRO GLU LYS CYS SEQRES 22 A 319 ALA ASP ASP LYS PRO TYR VAL PRO ILE TYR GLN VAL SER SEQRES 23 A 319 LYS GLU LYS ALA LYS SER LEU GLY LEU GLU TYR THR PRO SEQRES 24 A 319 LEU GLU VAL SER ILE LYS GLU THR VAL GLU SER LEU LYS SEQRES 25 A 319 GLU LYS LYS PHE ALA ASN LEU FORMUL 2 HOH *359(H2 O) HELIX 1 1 GLY A 17 ARG A 30 1 14 HELIX 2 2 ASP A 43 LYS A 46 5 4 HELIX 3 3 VAL A 47 LYS A 52 1 6 HELIX 4 4 GLY A 55 ARG A 59 1 5 HELIX 5 5 PHE A 73 GLN A 78 1 6 HELIX 6 6 ASP A 96 LEU A 101 1 6 HELIX 7 7 LEU A 101 LYS A 118 1 18 HELIX 8 8 SER A 130 VAL A 134 5 5 HELIX 9 9 ASP A 154 LYS A 160 1 7 HELIX 10 10 LEU A 163 ASN A 183 1 21 HELIX 11 11 ASN A 205 ASN A 216 1 12 HELIX 12 12 VAL A 231 ASN A 244 1 14 HELIX 13 13 TYR A 260 TYR A 271 1 12 HELIX 14 14 LYS A 294 LEU A 300 1 7 HELIX 15 15 PRO A 306 LYS A 321 1 16 SHEET 1 A 7 LEU A 60 LYS A 64 0 SHEET 2 A 7 THR A 33 VAL A 38 1 N VAL A 34 O GLN A 61 SHEET 3 A 7 VAL A 9 VAL A 12 1 N VAL A 10 O LYS A 35 SHEET 4 A 7 GLY A 82 HIS A 85 1 O PHE A 84 N CYS A 11 SHEET 5 A 7 ARG A 124 THR A 128 1 O VAL A 126 N VAL A 83 SHEET 6 A 7 MET A 187 PRO A 192 1 O VAL A 188 N LEU A 127 SHEET 7 A 7 GLY A 249 LEU A 253 1 O HIS A 251 N ASN A 191 SHEET 1 B 2 VAL A 146 VAL A 147 0 SHEET 2 B 2 GLN A 291 VAL A 292 1 O GLN A 291 N VAL A 147 SHEET 1 C 3 MET A 194 ILE A 196 0 SHEET 2 C 3 SER A 225 ASN A 230 1 O VAL A 229 N MET A 194 SHEET 3 C 3 ARG A 256 HIS A 259 -1 O ARG A 256 N TRP A 228 SHEET 1 D 2 THR A 220 PHE A 221 0 SHEET 2 D 2 LYS A 279 CYS A 280 1 O LYS A 279 N PHE A 221 CRYST1 37.797 76.565 106.045 90.00 90.00 90.00 P 21 21 21 4 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 0.026457 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009430 0.00000