HEADER PLANT PROTEIN 12-MAR-07 2P4H TITLE CRYSTAL STRUCTURE OF VESTITONE REDUCTASE FROM ALFALFA (MEDICAGO SATIVA TITLE 2 L.) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VESTITONE REDUCTASE; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MEDICAGO SATIVA; SOURCE 3 ORGANISM_TAXID: 3879; SOURCE 4 GENE: VESTITONE REDUCTASE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHIS8 KEYWDS NADPH-DEPENDENT REDUCTASE, ISOFLAVONOID, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,H.SHAO,R.A.DIXON REVDAT 3 21-FEB-24 2P4H 1 REMARK REVDAT 2 24-FEB-09 2P4H 1 VERSN REVDAT 1 15-MAY-07 2P4H 0 JRNL AUTH H.SHAO,R.A.DIXON,X.WANG JRNL TITL CRYSTAL STRUCTURE OF VESTITONE REDUCTASE FROM ALFALFA JRNL TITL 2 (MEDICAGO SATIVA L.). JRNL REF J.MOL.BIOL. V. 369 265 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17433362 JRNL DOI 10.1016/J.JMB.2007.03.040 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.61 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) (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 72486 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) : 0.188 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 7338 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 1059 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.008 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2405 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 542 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.30000 REMARK 3 B22 (A**2) : 4.65000 REMARK 3 B33 (A**2) : -2.27000 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) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.16 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2P4H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041954. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789, 0.9791, 0.9641 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 SI(111) AND SI(220) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77901 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 27.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39200 REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 6000, 0.1M MAGNESIUM CHLORIDE, REMARK 280 0.1M TRIS-HCL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 34.55150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.55150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.92500 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER. 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 APPLY THE FOLLOWING TO CHAINS: X 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 PRO X 40 REMARK 465 GLU X 41 REMARK 465 ARG X 42 REMARK 465 LYS X 43 REMARK 465 ASP X 90 REMARK 465 PHE X 91 REMARK 465 ALA X 92 REMARK 465 VAL X 93 REMARK 465 SER X 94 REMARK 465 GLU X 95 REMARK 465 PRO X 96 REMARK 465 GLU X 97 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 X 785 O HOH X 827 2.06 REMARK 500 O HOH X 829 O HOH X 861 2.07 REMARK 500 O HOH X 703 O HOH X 810 2.11 REMARK 500 O HOH X 767 O HOH X 789 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 SER X 128 -164.75 -108.21 REMARK 500 PHE X 135 57.09 -107.17 REMARK 500 ASP X 139 55.98 -97.26 REMARK 500 PRO X 192 -148.52 -87.98 REMARK 500 SER X 245 45.08 -71.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 2P4H X 5 326 UNP Q40316 Q40316_MEDSA 5 326 SEQRES 1 X 322 LYS GLY ARG VAL CYS VAL THR GLY GLY THR GLY PHE LEU SEQRES 2 X 322 GLY SER TRP ILE ILE LYS SER LEU LEU GLU ASN GLY TYR SEQRES 3 X 322 SER VAL ASN THR THR ILE ARG ALA ASP PRO GLU ARG LYS SEQRES 4 X 322 ARG ASP VAL SER PHE LEU THR ASN LEU PRO GLY ALA SER SEQRES 5 X 322 GLU LYS LEU HIS PHE PHE ASN ALA ASP LEU SER ASN PRO SEQRES 6 X 322 ASP SER PHE ALA ALA ALA ILE GLU GLY CYS VAL GLY ILE SEQRES 7 X 322 PHE HIS THR ALA SER PRO ILE ASP PHE ALA VAL SER GLU SEQRES 8 X 322 PRO GLU GLU ILE VAL THR LYS ARG THR VAL ASP GLY ALA SEQRES 9 X 322 LEU GLY ILE LEU LYS ALA CYS VAL ASN SER LYS THR VAL SEQRES 10 X 322 LYS ARG PHE ILE TYR THR SER SER GLY SER ALA VAL SER SEQRES 11 X 322 PHE ASN GLY LYS ASP LYS ASP VAL LEU ASP GLU SER ASP SEQRES 12 X 322 TRP SER ASP VAL ASP LEU LEU ARG SER VAL LYS PRO PHE SEQRES 13 X 322 GLY TRP ASN TYR ALA VAL SER LYS THR LEU ALA GLU LYS SEQRES 14 X 322 ALA VAL LEU GLU PHE GLY GLU GLN ASN GLY ILE ASP VAL SEQRES 15 X 322 VAL THR LEU ILE LEU PRO PHE ILE VAL GLY ARG PHE VAL SEQRES 16 X 322 CYS PRO LYS LEU PRO ASP SER ILE GLU LYS ALA LEU VAL SEQRES 17 X 322 LEU VAL LEU GLY LYS LYS GLU GLN ILE GLY VAL THR ARG SEQRES 18 X 322 PHE HIS MET VAL HIS VAL ASP ASP VAL ALA ARG ALA HIS SEQRES 19 X 322 ILE TYR LEU LEU GLU ASN SER VAL PRO GLY GLY ARG TYR SEQRES 20 X 322 ASN CYS SER PRO PHE ILE VAL PRO ILE GLU GLU MET SER SEQRES 21 X 322 GLN LEU LEU SER ALA LYS TYR PRO GLU TYR GLN ILE LEU SEQRES 22 X 322 THR VAL ASP GLU LEU LYS GLU ILE LYS GLY ALA ARG LEU SEQRES 23 X 322 PRO ASP LEU ASN THR LYS LYS LEU VAL ASP ALA GLY PHE SEQRES 24 X 322 ASP PHE LYS TYR THR ILE GLU ASP MET PHE ASP ASP ALA SEQRES 25 X 322 ILE GLN CYS CYS LYS GLU LYS GLY TYR LEU FORMUL 2 HOH *542(H2 O) HELIX 1 1 GLY X 15 ASN X 28 1 14 HELIX 2 2 VAL X 46 ASN X 51 1 6 HELIX 3 3 GLY X 54 LYS X 58 1 5 HELIX 4 4 ASN X 68 SER X 71 5 4 HELIX 5 5 PHE X 72 GLU X 77 1 6 HELIX 6 6 GLU X 98 VAL X 116 1 19 HELIX 7 7 SER X 131 VAL X 133 5 3 HELIX 8 8 ASP X 150 LYS X 158 1 9 HELIX 9 9 GLY X 161 ASN X 182 1 22 HELIX 10 10 PRO X 204 LEU X 211 1 8 HELIX 11 11 LEU X 211 GLY X 216 1 6 HELIX 12 12 LYS X 217 ILE X 221 5 5 HELIX 13 13 VAL X 231 ASN X 244 1 14 HELIX 14 14 ILE X 260 TYR X 271 1 12 HELIX 15 15 THR X 295 ALA X 301 1 7 HELIX 16 16 THR X 308 LYS X 323 1 16 SHEET 1 A 7 LEU X 59 PHE X 61 0 SHEET 2 A 7 SER X 31 THR X 35 1 N VAL X 32 O HIS X 60 SHEET 3 A 7 ARG X 7 THR X 11 1 N VAL X 10 O ASN X 33 SHEET 4 A 7 GLY X 81 HIS X 84 1 O PHE X 83 N CYS X 9 SHEET 5 A 7 ARG X 123 SER X 129 1 O ILE X 125 N ILE X 82 SHEET 6 A 7 VAL X 186 LEU X 191 1 O LEU X 189 N SER X 128 SHEET 7 A 7 GLY X 249 ASN X 252 1 O TYR X 251 N ILE X 190 SHEET 1 B 2 VAL X 142 LEU X 143 0 SHEET 2 B 2 ASP X 292 LEU X 293 1 O ASP X 292 N LEU X 143 SHEET 1 C 3 PHE X 193 VAL X 195 0 SHEET 2 C 3 VAL X 223 HIS X 230 1 O VAL X 229 N VAL X 195 SHEET 3 C 3 PHE X 256 PRO X 259 -1 O VAL X 258 N PHE X 226 SHEET 1 D 3 PHE X 193 VAL X 195 0 SHEET 2 D 3 VAL X 223 HIS X 230 1 O VAL X 229 N VAL X 195 SHEET 3 D 3 ALA X 288 ARG X 289 1 O ALA X 288 N THR X 224 CRYST1 69.103 91.850 63.186 90.00 90.00 90.00 P 21 21 2 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 0.014471 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015826 0.00000