HEADER OXIDOREDUCTASE 10-JUL-18 6H0N TITLE THE STRUCTURE OF WILD-TYPE ARABIDOPSIS THALIANA UDP-APIOSE/UDP-XYLOSE TITLE 2 SYNTHASE IN COMPLEX WITH NAD+ AND UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-D-APIOSE/UDP-D-XYLOSE SYNTHASE 1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AXS1, AT2G27860, F15K20.4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENZYME CATALYSIS, GLYCOBIOLOGY, SHORT-CHAIN DEHYDROGENASES/REDUCTASES KEYWDS 2 (SDR), ALDOL CLEAVAGE, SUBSTRATE-ASSISTED REACTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SAVINO,A.MATTEVI REVDAT 3 17-JAN-24 6H0N 1 REMARK REVDAT 2 06-MAY-20 6H0N 1 JRNL REVDAT 1 23-OCT-19 6H0N 0 JRNL AUTH S.SAVINO,A.J.E.BORG,A.DENNIG,M.PFEIFFER,F.DE GIORGI,H.WEBER, JRNL AUTH 2 K.D.DUBEY,C.ROVIRA,A.MATTEVI,B.NIDETZKY JRNL TITL DECIPHERING THE ENZYMATIC MECHANISM OF SUGAR RING JRNL TITL 2 CONTRACTION IN UDP-APIOSE BIOSYNTHESIS. JRNL REF NAT CATAL V. 2 1115 2019 JRNL REFN ESSN 2520-1158 JRNL PMID 31844840 JRNL DOI 10.1038/S41929-019-0382-8 REMARK 2 REMARK 2 RESOLUTION. 3.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 126.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 30595 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 + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1640 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2057 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.3690 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5840 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 148 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : 1.54000 REMARK 3 B33 (A**2) : -5.01000 REMARK 3 B12 (A**2) : 0.77000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.611 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.345 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.310 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.584 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6124 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5553 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8354 ; 1.824 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12878 ; 1.076 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 742 ; 7.363 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 270 ;39.309 ;24.111 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 983 ;17.064 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;20.381 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 941 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6713 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1227 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2983 ; 5.408 ; 7.786 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2982 ; 5.407 ; 7.785 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3720 ; 7.935 ;11.686 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3721 ; 7.934 ;11.687 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3141 ; 5.830 ; 8.147 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3140 ; 5.830 ; 8.148 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4635 ; 8.850 ;12.054 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6847 ;10.782 ;91.695 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6848 ;10.782 ;91.688 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 8 384 B 8 384 23974 0.08 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6H0N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200010854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.003680 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32264 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.020 REMARK 200 RESOLUTION RANGE LOW (A) : 126.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3SLG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M SODIUM PHOSPHATE, 0.8 M REMARK 280 POTASSIUM PHOSPHATE, 0.1 M SODIUM-HEPES, PH 7.5, EVAPORATION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.56333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.28167 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.28167 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.56333 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: 8170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASN A 3 REMARK 465 GLY A 4 REMARK 465 ALA A 5 REMARK 465 ASN A 6 REMARK 465 ARG A 7 REMARK 465 LYS A 385 REMARK 465 PRO A 386 REMARK 465 VAL A 387 REMARK 465 ALA A 388 REMARK 465 SER A 389 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASN B 3 REMARK 465 GLY B 4 REMARK 465 ALA B 5 REMARK 465 ASN B 6 REMARK 465 PRO B 61 REMARK 465 ASP B 62 REMARK 465 THR B 63 REMARK 465 VAL B 64 REMARK 465 GLU B 65 REMARK 465 TRP B 66 REMARK 465 SER B 67 REMARK 465 GLY B 68 REMARK 465 LYS B 385 REMARK 465 PRO B 386 REMARK 465 VAL B 387 REMARK 465 ALA B 388 REMARK 465 SER B 389 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 GLU A 60 CG CD OE1 OE2 REMARK 470 VAL A 64 CG1 CG2 REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 GLU A 231 CG CD OE1 OE2 REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 GLU A 315 CG CD OE1 OE2 REMARK 470 GLU A 319 CG CD OE1 OE2 REMARK 470 LYS A 328 CG CD CE NZ REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 LYS A 380 CG CD CE NZ REMARK 470 LYS A 381 CG CD CE NZ REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 GLN B 16 CG CD OE1 NE2 REMARK 470 LYS B 153 CG CD CE NZ REMARK 470 SER B 320 OG REMARK 470 LYS B 328 CG CD CE NZ REMARK 470 GLU B 329 CG CD OE1 OE2 REMARK 470 LYS B 357 CG CD CE NZ REMARK 470 LYS B 380 CG CD CE NZ 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 OD2 ASP B 227 OH TYR B 375 1.63 REMARK 500 NZ LYS A 36 OE1 GLU A 270 1.72 REMARK 500 OD2 ASP A 227 OH TYR A 375 2.01 REMARK 500 NZ LYS A 340 O HOH A 501 2.10 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 ASP A 80 109.27 -161.04 REMARK 500 ALA A 98 135.88 -176.65 REMARK 500 ARG A 108 57.67 -118.76 REMARK 500 SER A 138 -132.39 -96.92 REMARK 500 PRO A 152 154.38 -49.18 REMARK 500 ALA A 162 -33.44 -38.82 REMARK 500 ASP A 221 -127.60 62.25 REMARK 500 ILE A 226 -72.55 -129.67 REMARK 500 ASN A 294 56.95 -90.27 REMARK 500 ASP B 11 20.32 -60.58 REMARK 500 ASP B 80 104.95 -168.83 REMARK 500 ALA B 98 135.85 -177.06 REMARK 500 ARG B 108 58.42 -118.42 REMARK 500 SER B 138 -133.02 -97.42 REMARK 500 ALA B 162 -33.03 -39.24 REMARK 500 PRO B 218 -73.89 -39.34 REMARK 500 ARG B 219 34.54 -92.44 REMARK 500 ASP B 221 -127.72 62.48 REMARK 500 ILE B 226 -65.75 -139.75 REMARK 500 ASN B 294 56.40 -90.35 REMARK 500 ALA B 317 -169.67 -72.85 REMARK 500 MET B 345 -17.12 86.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 350 0.10 SIDE CHAIN 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 NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 403 DBREF 6H0N A 1 389 UNP Q9ZUY6 AXS1_ARATH 1 389 DBREF 6H0N B 1 389 UNP Q9ZUY6 AXS1_ARATH 1 389 SEQRES 1 A 389 MET ALA ASN GLY ALA ASN ARG VAL ASP LEU ASP GLY LYS SEQRES 2 A 389 PRO ILE GLN PRO LEU THR ILE CYS MET ILE GLY ALA GLY SEQRES 3 A 389 GLY PHE ILE GLY SER HIS LEU CYS GLU LYS LEU LEU THR SEQRES 4 A 389 GLU THR PRO HIS LYS VAL LEU ALA LEU ASP VAL TYR ASN SEQRES 5 A 389 ASP LYS ILE LYS HIS LEU LEU GLU PRO ASP THR VAL GLU SEQRES 6 A 389 TRP SER GLY ARG ILE GLN PHE HIS ARG ILE ASN ILE LYS SEQRES 7 A 389 HIS ASP SER ARG LEU GLU GLY LEU VAL LYS MET ALA ASP SEQRES 8 A 389 LEU ILE ILE ASN LEU ALA ALA ILE CYS THR PRO ALA ASP SEQRES 9 A 389 TYR ASN THR ARG PRO LEU ASP THR ILE TYR SER ASN PHE SEQRES 10 A 389 ILE ASP ALA LEU PRO VAL VAL LYS TYR CYS SER GLU ASN SEQRES 11 A 389 ASN LYS ARG LEU ILE HIS PHE SER THR CYS GLU VAL TYR SEQRES 12 A 389 GLY LYS THR ILE GLY SER PHE LEU PRO LYS ASP HIS PRO SEQRES 13 A 389 LEU ARG ASP ASP PRO ALA PHE TYR VAL LEU LYS GLU ASP SEQRES 14 A 389 ILE SER PRO CYS ILE PHE GLY SER ILE GLU LYS GLN ARG SEQRES 15 A 389 TRP SER TYR ALA CYS ALA LYS GLN LEU ILE GLU ARG LEU SEQRES 16 A 389 VAL TYR ALA GLU GLY ALA GLU ASN GLY LEU GLU PHE THR SEQRES 17 A 389 ILE VAL ARG PRO PHE ASN TRP ILE GLY PRO ARG MET ASP SEQRES 18 A 389 PHE ILE PRO GLY ILE ASP GLY PRO SER GLU GLY VAL PRO SEQRES 19 A 389 ARG VAL LEU ALA CYS PHE SER ASN ASN LEU LEU ARG ARG SEQRES 20 A 389 GLU PRO LEU LYS LEU VAL ASP GLY GLY GLU SER GLN ARG SEQRES 21 A 389 THR PHE VAL TYR ILE ASN ASP ALA ILE GLU ALA VAL LEU SEQRES 22 A 389 LEU MET ILE GLU ASN PRO GLU ARG ALA ASN GLY HIS ILE SEQRES 23 A 389 PHE ASN VAL GLY ASN PRO ASN ASN GLU VAL THR VAL ARG SEQRES 24 A 389 GLN LEU ALA GLU MET MET THR GLU VAL TYR ALA LYS VAL SEQRES 25 A 389 SER GLY GLU GLY ALA ILE GLU SER PRO THR VAL ASP VAL SEQRES 26 A 389 SER SER LYS GLU PHE TYR GLY GLU GLY TYR ASP ASP SER SEQRES 27 A 389 ASP LYS ARG ILE PRO ASP MET THR ILE ILE ASN ARG GLN SEQRES 28 A 389 LEU GLY TRP ASN PRO LYS THR SER LEU TRP ASP LEU LEU SEQRES 29 A 389 GLU SER THR LEU THR TYR GLN HIS ARG THR TYR ALA GLU SEQRES 30 A 389 ALA VAL LYS LYS ALA THR SER LYS PRO VAL ALA SER SEQRES 1 B 389 MET ALA ASN GLY ALA ASN ARG VAL ASP LEU ASP GLY LYS SEQRES 2 B 389 PRO ILE GLN PRO LEU THR ILE CYS MET ILE GLY ALA GLY SEQRES 3 B 389 GLY PHE ILE GLY SER HIS LEU CYS GLU LYS LEU LEU THR SEQRES 4 B 389 GLU THR PRO HIS LYS VAL LEU ALA LEU ASP VAL TYR ASN SEQRES 5 B 389 ASP LYS ILE LYS HIS LEU LEU GLU PRO ASP THR VAL GLU SEQRES 6 B 389 TRP SER GLY ARG ILE GLN PHE HIS ARG ILE ASN ILE LYS SEQRES 7 B 389 HIS ASP SER ARG LEU GLU GLY LEU VAL LYS MET ALA ASP SEQRES 8 B 389 LEU ILE ILE ASN LEU ALA ALA ILE CYS THR PRO ALA ASP SEQRES 9 B 389 TYR ASN THR ARG PRO LEU ASP THR ILE TYR SER ASN PHE SEQRES 10 B 389 ILE ASP ALA LEU PRO VAL VAL LYS TYR CYS SER GLU ASN SEQRES 11 B 389 ASN LYS ARG LEU ILE HIS PHE SER THR CYS GLU VAL TYR SEQRES 12 B 389 GLY LYS THR ILE GLY SER PHE LEU PRO LYS ASP HIS PRO SEQRES 13 B 389 LEU ARG ASP ASP PRO ALA PHE TYR VAL LEU LYS GLU ASP SEQRES 14 B 389 ILE SER PRO CYS ILE PHE GLY SER ILE GLU LYS GLN ARG SEQRES 15 B 389 TRP SER TYR ALA CYS ALA LYS GLN LEU ILE GLU ARG LEU SEQRES 16 B 389 VAL TYR ALA GLU GLY ALA GLU ASN GLY LEU GLU PHE THR SEQRES 17 B 389 ILE VAL ARG PRO PHE ASN TRP ILE GLY PRO ARG MET ASP SEQRES 18 B 389 PHE ILE PRO GLY ILE ASP GLY PRO SER GLU GLY VAL PRO SEQRES 19 B 389 ARG VAL LEU ALA CYS PHE SER ASN ASN LEU LEU ARG ARG SEQRES 20 B 389 GLU PRO LEU LYS LEU VAL ASP GLY GLY GLU SER GLN ARG SEQRES 21 B 389 THR PHE VAL TYR ILE ASN ASP ALA ILE GLU ALA VAL LEU SEQRES 22 B 389 LEU MET ILE GLU ASN PRO GLU ARG ALA ASN GLY HIS ILE SEQRES 23 B 389 PHE ASN VAL GLY ASN PRO ASN ASN GLU VAL THR VAL ARG SEQRES 24 B 389 GLN LEU ALA GLU MET MET THR GLU VAL TYR ALA LYS VAL SEQRES 25 B 389 SER GLY GLU GLY ALA ILE GLU SER PRO THR VAL ASP VAL SEQRES 26 B 389 SER SER LYS GLU PHE TYR GLY GLU GLY TYR ASP ASP SER SEQRES 27 B 389 ASP LYS ARG ILE PRO ASP MET THR ILE ILE ASN ARG GLN SEQRES 28 B 389 LEU GLY TRP ASN PRO LYS THR SER LEU TRP ASP LEU LEU SEQRES 29 B 389 GLU SER THR LEU THR TYR GLN HIS ARG THR TYR ALA GLU SEQRES 30 B 389 ALA VAL LYS LYS ALA THR SER LYS PRO VAL ALA SER HET NAD A 401 44 HET UDP A 402 25 HET PO4 A 403 5 HET NAD B 401 44 HET UDP B 402 25 HET PO4 B 403 5 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM PO4 PHOSPHATE ION FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 5 PO4 2(O4 P 3-) FORMUL 9 HOH *23(H2 O) HELIX 1 AA1 GLY A 27 THR A 41 1 15 HELIX 2 AA2 ASN A 52 LEU A 59 5 8 HELIX 3 AA3 SER A 81 ALA A 90 1 10 HELIX 4 AA4 THR A 101 TYR A 105 5 5 HELIX 5 AA5 ARG A 108 PHE A 117 1 10 HELIX 6 AA6 ALA A 120 ASN A 130 1 11 HELIX 7 AA7 THR A 139 TYR A 143 5 5 HELIX 8 AA8 THR A 146 LEU A 151 5 6 HELIX 9 AA9 HIS A 155 PHE A 163 5 9 HELIX 10 AB1 ARG A 182 ASN A 203 1 22 HELIX 11 AB2 ARG A 235 ARG A 246 1 12 HELIX 12 AB3 GLY A 255 GLU A 257 5 3 HELIX 13 AB4 ILE A 265 ASN A 278 1 14 HELIX 14 AB5 ASN A 278 ASN A 283 1 6 HELIX 15 AB6 VAL A 298 GLY A 314 1 17 HELIX 16 AB7 SER A 326 GLY A 332 1 7 HELIX 17 AB8 MET A 345 GLY A 353 1 9 HELIX 18 AB9 SER A 359 ALA A 382 1 24 HELIX 19 AC1 GLY B 27 THR B 41 1 15 HELIX 20 AC2 ASN B 52 LEU B 59 5 8 HELIX 21 AC3 ARG B 82 ALA B 90 1 9 HELIX 22 AC4 THR B 101 TYR B 105 5 5 HELIX 23 AC5 ARG B 108 PHE B 117 1 10 HELIX 24 AC6 ALA B 120 ASN B 130 1 11 HELIX 25 AC7 THR B 139 TYR B 143 5 5 HELIX 26 AC8 THR B 146 LEU B 151 5 6 HELIX 27 AC9 HIS B 155 TYR B 164 5 10 HELIX 28 AD1 ARG B 182 ASN B 203 1 22 HELIX 29 AD2 ARG B 235 ARG B 246 1 12 HELIX 30 AD3 GLY B 255 GLU B 257 5 3 HELIX 31 AD4 ILE B 265 ASN B 278 1 14 HELIX 32 AD5 ASN B 278 ASN B 283 1 6 HELIX 33 AD6 VAL B 298 GLY B 314 1 17 HELIX 34 AD7 SER B 326 GLY B 332 1 7 HELIX 35 AD8 MET B 345 LEU B 352 1 8 HELIX 36 AD9 SER B 359 SER B 384 1 26 SHEET 1 AA1 7 ILE A 70 ARG A 74 0 SHEET 2 AA1 7 LYS A 44 ASP A 49 1 N ALA A 47 O HIS A 73 SHEET 3 AA1 7 THR A 19 ILE A 23 1 N ILE A 20 O LEU A 46 SHEET 4 AA1 7 LEU A 92 ASN A 95 1 O ILE A 94 N ILE A 23 SHEET 5 AA1 7 ARG A 133 PHE A 137 1 O ARG A 133 N ILE A 93 SHEET 6 AA1 7 PHE A 207 PRO A 212 1 O THR A 208 N HIS A 136 SHEET 7 AA1 7 ILE A 286 VAL A 289 1 O PHE A 287 N ARG A 211 SHEET 1 AA2 2 VAL A 165 LEU A 166 0 SHEET 2 AA2 2 ILE A 342 PRO A 343 1 O ILE A 342 N LEU A 166 SHEET 1 AA3 2 CYS A 173 PHE A 175 0 SHEET 2 AA3 2 CYS B 173 PHE B 175 -1 O PHE B 175 N CYS A 173 SHEET 1 AA4 2 TRP A 215 ILE A 216 0 SHEET 2 AA4 2 VAL A 263 TYR A 264 1 O VAL A 263 N ILE A 216 SHEET 1 AA5 2 LEU A 250 VAL A 253 0 SHEET 2 AA5 2 THR A 322 VAL A 325 1 O VAL A 323 N LEU A 252 SHEET 1 AA6 2 GLN A 259 THR A 261 0 SHEET 2 AA6 2 GLU A 295 THR A 297 -1 O VAL A 296 N ARG A 260 SHEET 1 AA7 7 ILE B 70 ARG B 74 0 SHEET 2 AA7 7 LYS B 44 ASP B 49 1 N ALA B 47 O HIS B 73 SHEET 3 AA7 7 THR B 19 ILE B 23 1 N ILE B 20 O LEU B 46 SHEET 4 AA7 7 LEU B 92 ASN B 95 1 O ILE B 94 N ILE B 23 SHEET 5 AA7 7 ARG B 133 PHE B 137 1 O ARG B 133 N ILE B 93 SHEET 6 AA7 7 PHE B 207 PRO B 212 1 O THR B 208 N HIS B 136 SHEET 7 AA7 7 ILE B 286 VAL B 289 1 O PHE B 287 N ARG B 211 SHEET 1 AA8 2 TRP B 215 ILE B 216 0 SHEET 2 AA8 2 VAL B 263 TYR B 264 1 O VAL B 263 N ILE B 216 SHEET 1 AA9 2 LEU B 250 VAL B 253 0 SHEET 2 AA9 2 THR B 322 VAL B 325 1 O VAL B 323 N LEU B 252 SHEET 1 AB1 2 GLN B 259 THR B 261 0 SHEET 2 AB1 2 GLU B 295 THR B 297 -1 O VAL B 296 N ARG B 260 SITE 1 AC1 24 GLY A 24 GLY A 26 GLY A 27 PHE A 28 SITE 2 AC1 24 ILE A 29 ASP A 49 VAL A 50 ILE A 75 SITE 3 AC1 24 ASN A 76 ILE A 77 LEU A 96 ALA A 97 SITE 4 AC1 24 ALA A 98 CYS A 100 PHE A 137 SER A 138 SITE 5 AC1 24 THR A 139 TYR A 185 LYS A 189 PRO A 212 SITE 6 AC1 24 ASN A 214 TRP A 215 ARG A 235 PO4 A 403 SITE 1 AC2 18 PRO A 102 GLU A 141 ARG A 182 ASN A 214 SITE 2 AC2 18 ARG A 235 VAL A 236 CYS A 239 LYS A 251 SITE 3 AC2 18 LEU A 252 VAL A 253 ARG A 260 VAL A 298 SITE 4 AC2 18 PHE A 330 TYR A 331 TYR A 335 ASP A 337 SITE 5 AC2 18 ARG A 341 PO4 A 403 SITE 1 AC3 8 CYS A 100 TYR A 105 THR A 139 GLU A 141 SITE 2 AC3 8 TYR A 185 ARG A 235 NAD A 401 UDP A 402 SITE 1 AC4 22 GLY B 24 GLY B 26 GLY B 27 PHE B 28 SITE 2 AC4 22 ILE B 29 ASP B 49 ILE B 75 ASN B 76 SITE 3 AC4 22 ILE B 77 LEU B 96 ALA B 97 ALA B 98 SITE 4 AC4 22 CYS B 100 PHE B 137 SER B 138 THR B 139 SITE 5 AC4 22 TYR B 185 LYS B 189 PRO B 212 TRP B 215 SITE 6 AC4 22 ARG B 235 PO4 B 403 SITE 1 AC5 18 PRO B 102 GLU B 141 ARG B 182 ASN B 214 SITE 2 AC5 18 ARG B 235 VAL B 236 CYS B 239 LYS B 251 SITE 3 AC5 18 LEU B 252 VAL B 253 ARG B 260 VAL B 298 SITE 4 AC5 18 PHE B 330 TYR B 331 TYR B 335 ASP B 337 SITE 5 AC5 18 ARG B 341 PO4 B 403 SITE 1 AC6 8 CYS B 100 TYR B 105 THR B 139 GLU B 141 SITE 2 AC6 8 TYR B 185 ARG B 235 NAD B 401 UDP B 402 CRYST1 146.028 146.028 132.845 90.00 90.00 120.00 P 32 2 1 12 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 0.006848 0.003954 0.000000 0.00000 SCALE2 0.000000 0.007907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007528 0.00000