HEADER TRANSFERASE 03-AUG-15 5D0N TITLE CRYSTAL STRUCTURE OF MAIZE PDRP BOUND WITH AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE, PHOSPHATE DIKINASE REGULATORY PROTEIN, COMPND 3 CHLOROPLASTIC; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 38-426; COMPND 6 SYNONYM: BIFUNCTIONAL DIKINASE REGULATORY PROTEIN,BFRP,PYRUVATE,PI COMPND 7 DIKINASE REGULATORY PROTEIN,PPDK REGULATORY PROTEIN; COMPND 8 EC: 2.7.11.32,2.7.4.27; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_COMMON: MAIZE; SOURCE 4 ORGANISM_TAXID: 4577; SOURCE 5 GENE: PDRP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS PDRP, REVERSIBLE PHOSPHORYLATION, C4 PHOTOSYNTHESIS, ADP-DEPENDENT KEYWDS 2 PROTEIN KINASE/PI-DEPENDENT PROTEIN PHOSPHATASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.JIANG,Z.CHEN REVDAT 3 23-OCT-24 5D0N 1 REMARK SSBOND REVDAT 2 09-MAR-16 5D0N 1 EXPDTA REVDAT 1 24-FEB-16 5D0N 0 JRNL AUTH L.JIANG,Y.B.CHEN,J.ZHENG,Z.CHEN,Y.LIU,Y.TAO,W.WU,Z.CHEN, JRNL AUTH 2 B.C.WANG JRNL TITL STRUCTURAL BASIS OF REVERSIBLE PHOSPHORYLATION BY MAIZE JRNL TITL 2 PYRUVATE ORTHOPHOSPHATE DIKINASE REGULATORY PROTEIN JRNL REF PLANT PHYSIOL. V. 170 732 2016 JRNL REFN ESSN 1532-2548 JRNL PMID 26620526 JRNL DOI 10.1104/PP.15.01709 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 14922 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 785 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 980 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.3970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2030 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.404 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.287 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.201 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.624 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2095 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1939 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2860 ; 1.443 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4453 ; 0.959 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 271 ; 6.776 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;43.228 ;25.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 317 ;18.975 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;17.836 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 337 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2385 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 441 ; 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): 1093 ; 3.164 ; 5.872 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1092 ; 3.157 ; 5.869 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1361 ; 5.562 ; 8.778 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1362 ; 5.563 ; 8.781 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1000 ; 2.598 ; 6.064 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1001 ; 2.596 ; 6.064 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1499 ; 4.583 ; 8.956 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2373 ; 8.852 ;46.524 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2372 ; 8.852 ;46.535 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 5D0N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DATA IS COLLECTED AT SSRF REMARK 200 BEAMLINE BL18U REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15812 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 54.10 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 59.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 49.60 REMARK 200 R MERGE FOR SHELL (I) : 0.53600 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: SAD 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 (%): 75.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, BICINE AND 2% DIOXANE, PH 7, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 Y,X,-Z REMARK 290 14555 -Y,-X,-Z REMARK 290 15555 Y,-X,Z REMARK 290 16555 -Y,X,Z REMARK 290 17555 X,Z,-Y REMARK 290 18555 -X,Z,Y REMARK 290 19555 -X,-Z,-Y REMARK 290 20555 X,-Z,Y REMARK 290 21555 Z,Y,-X REMARK 290 22555 Z,-Y,X REMARK 290 23555 -Z,Y,X REMARK 290 24555 -Z,-Y,-X 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 175.34200 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 601 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 628 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 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 SER A 21 REMARK 465 SER A 22 REMARK 465 GLY A 23 REMARK 465 VAL A 24 REMARK 465 ASP A 25 REMARK 465 LEU A 26 REMARK 465 GLY A 27 REMARK 465 THR A 28 REMARK 465 GLU A 29 REMARK 465 ASN A 30 REMARK 465 LEU A 31 REMARK 465 TYR A 32 REMARK 465 PHE A 33 REMARK 465 GLN A 34 REMARK 465 SER A 35 REMARK 465 ASN A 36 REMARK 465 ALA A 37 REMARK 465 ALA A 38 REMARK 465 LEU A 39 REMARK 465 THR A 40 REMARK 465 ARG A 41 REMARK 465 ALA A 42 REMARK 465 VAL A 43 REMARK 465 GLU A 44 REMARK 465 SER A 45 REMARK 465 PRO A 46 REMARK 465 GLY A 47 REMARK 465 GLN A 48 REMARK 465 SER A 49 REMARK 465 GLN A 50 REMARK 465 SER A 51 REMARK 465 ASP A 52 REMARK 465 ASP A 53 REMARK 465 ALA A 54 REMARK 465 PRO A 55 REMARK 465 PRO A 56 REMARK 465 PRO A 57 REMARK 465 ARG A 58 REMARK 465 SER A 59 REMARK 465 GLY A 60 REMARK 465 GLU A 61 REMARK 465 ALA A 62 REMARK 465 ALA A 63 REMARK 465 SER A 64 REMARK 465 SER A 65 REMARK 465 LEU A 66 REMARK 465 ALA A 67 REMARK 465 PRO A 68 REMARK 465 ARG A 69 REMARK 465 ALA A 70 REMARK 465 SER A 71 REMARK 465 SER A 72 REMARK 465 HIS A 73 REMARK 465 LEU A 74 REMARK 465 ASP A 75 REMARK 465 ARG A 76 REMARK 465 TRP A 77 REMARK 465 SER A 78 REMARK 465 ARG A 79 REMARK 465 SER A 80 REMARK 465 ARG A 81 REMARK 465 ALA A 82 REMARK 465 LEU A 83 REMARK 465 ARG A 84 REMARK 465 SER A 85 REMARK 465 GLY A 86 REMARK 465 HIS A 87 REMARK 465 ARG A 88 REMARK 465 PRO A 89 REMARK 465 ALA A 90 REMARK 465 LEU A 91 REMARK 465 ASN A 92 REMARK 465 ARG A 93 REMARK 465 ALA A 94 REMARK 465 ALA A 95 REMARK 465 LEU A 96 REMARK 465 SER A 97 REMARK 465 SER A 98 REMARK 465 ALA A 99 REMARK 465 SER A 100 REMARK 465 VAL A 101 REMARK 465 SER A 102 REMARK 465 ALA A 103 REMARK 465 PRO A 104 REMARK 465 PRO A 105 REMARK 465 VAL A 106 REMARK 465 ILE A 107 REMARK 465 LYS A 108 REMARK 465 SER A 109 REMARK 465 PRO A 110 REMARK 465 ARG A 111 REMARK 465 PRO A 112 REMARK 465 GLU A 113 REMARK 465 ASP A 114 REMARK 465 ALA A 115 REMARK 465 ALA A 116 REMARK 465 VAL A 117 REMARK 465 ALA A 118 REMARK 465 VAL A 119 REMARK 465 GLU A 120 REMARK 465 ASP A 121 REMARK 465 GLY A 122 REMARK 465 GLU A 123 REMARK 465 ASP A 124 REMARK 465 ASP A 125 REMARK 465 ALA A 130 REMARK 465 GLU A 131 REMARK 465 ARG A 132 REMARK 465 ASP A 133 REMARK 465 ALA A 134 REMARK 465 LEU A 346 REMARK 465 GLN A 347 REMARK 465 ALA A 348 REMARK 465 ILE A 349 REMARK 465 ARG A 350 REMARK 465 LYS A 351 REMARK 465 THR A 352 REMARK 465 ARG A 353 REMARK 465 ALA A 354 REMARK 465 LYS A 355 REMARK 465 THR A 356 REMARK 465 LEU A 357 REMARK 465 GLY A 358 REMARK 465 PHE A 359 REMARK 465 ASP A 360 REMARK 465 GLY A 361 REMARK 465 ARG A 362 REMARK 465 GLN A 363 REMARK 465 SER A 364 REMARK 465 ASN A 365 REMARK 465 TYR A 366 REMARK 465 ALA A 367 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 138 CD CE NZ REMARK 470 ASN A 156 ND2 REMARK 470 LEU A 180 CD1 REMARK 470 ILE A 188 CD1 REMARK 470 LYS A 192 CG CD CE NZ REMARK 470 LYS A 196 CG CD CE NZ REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 ARG A 230 CZ NH1 NH2 REMARK 470 ILE A 236 CD1 REMARK 470 ILE A 240 CD1 REMARK 470 ARG A 254 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 257 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 269 CD1 REMARK 470 ILE A 273 CD1 REMARK 470 ARG A 286 CZ NH1 NH2 REMARK 470 ILE A 304 CD1 REMARK 470 LYS A 312 NZ REMARK 470 ILE A 341 CD1 REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 376 CD1 CD2 REMARK 470 LYS A 397 CD CE NZ REMARK 470 LYS A 414 CG CD CE NZ REMARK 470 LYS A 424 CE NZ REMARK 470 ARG A 425 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 THR A 226 124.54 -170.84 REMARK 500 ARG A 254 -0.77 61.89 REMARK 500 ALA A 279 50.70 -107.47 REMARK 500 LYS A 335 -17.17 106.48 REMARK 500 GLN A 385 -29.18 -39.55 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 632 DISTANCE = 5.86 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AMP A 501 O1P REMARK 620 2 AMP A 501 O3P 49.9 REMARK 620 3 AMP A 501 O5' 53.6 50.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D1F RELATED DB: PDB DBREF 5D0N A 38 426 UNP Q195N6 PDRP1_MAIZE 38 426 SEQADV 5D0N MET A 14 UNP Q195N6 INITIATING METHIONINE SEQADV 5D0N HIS A 15 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N HIS A 16 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N HIS A 17 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N HIS A 18 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N HIS A 19 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N HIS A 20 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N SER A 21 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N SER A 22 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N GLY A 23 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N VAL A 24 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N ASP A 25 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N LEU A 26 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N GLY A 27 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N THR A 28 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N GLU A 29 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N ASN A 30 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N LEU A 31 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N TYR A 32 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N PHE A 33 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N GLN A 34 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N SER A 35 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N ASN A 36 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N ALA A 37 UNP Q195N6 EXPRESSION TAG SEQADV 5D0N VAL A 119 UNP Q195N6 ALA 119 ENGINEERED MUTATION SEQADV 5D0N SER A 251 UNP Q195N6 PHE 251 ENGINEERED MUTATION SEQADV 5D0N ALA A 279 UNP Q195N6 VAL 279 ENGINEERED MUTATION SEQADV 5D0N LEU A 284 UNP Q195N6 PHE 284 ENGINEERED MUTATION SEQADV 5D0N ASP A 323 UNP Q195N6 ALA 323 ENGINEERED MUTATION SEQADV 5D0N ALA A 348 UNP Q195N6 GLY 348 ENGINEERED MUTATION SEQADV 5D0N ALA A 384 UNP Q195N6 VAL 384 ENGINEERED MUTATION SEQADV 5D0N SER A 388 UNP Q195N6 TRP 388 ENGINEERED MUTATION SEQRES 1 A 413 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 413 GLY THR GLU ASN LEU TYR PHE GLN SER ASN ALA ALA LEU SEQRES 3 A 413 THR ARG ALA VAL GLU SER PRO GLY GLN SER GLN SER ASP SEQRES 4 A 413 ASP ALA PRO PRO PRO ARG SER GLY GLU ALA ALA SER SER SEQRES 5 A 413 LEU ALA PRO ARG ALA SER SER HIS LEU ASP ARG TRP SER SEQRES 6 A 413 ARG SER ARG ALA LEU ARG SER GLY HIS ARG PRO ALA LEU SEQRES 7 A 413 ASN ARG ALA ALA LEU SER SER ALA SER VAL SER ALA PRO SEQRES 8 A 413 PRO VAL ILE LYS SER PRO ARG PRO GLU ASP ALA ALA VAL SEQRES 9 A 413 ALA VAL GLU ASP GLY GLU ASP ASP ASP VAL CYS GLU ALA SEQRES 10 A 413 GLU ARG ASP ALA ALA ALA GLY LYS ALA ILE TYR ILE VAL SEQRES 11 A 413 SER ASP GLY THR GLY TRP THR ALA GLU HIS SER VAL ASN SEQRES 12 A 413 ALA ALA LEU GLY GLN PHE GLU ASN CYS LEU ALA ASP ARG SEQRES 13 A 413 GLY CYS ALA VAL ASN THR HIS LEU PHE SER LEU ILE ASP SEQRES 14 A 413 ASP MET ASP ARG LEU ILE GLU VAL ILE LYS GLN ALA ALA SEQRES 15 A 413 LYS GLU GLY ALA LEU VAL LEU TYR THR LEU ALA ASP PRO SEQRES 16 A 413 SER MET ALA GLU ALA THR LYS LYS ALA CYS ASP PHE TRP SEQRES 17 A 413 GLY VAL PRO CYS THR ASP VAL LEU ARG PRO THR VAL GLU SEQRES 18 A 413 ALA ILE ALA SER HIS ILE GLY VAL ALA PRO SER GLY ILE SEQRES 19 A 413 PRO ARG SER SER PRO SER ARG ASN GLY ARG LEU SER GLU SEQRES 20 A 413 ASP TYR PHE GLN ARG ILE ASP ALA ILE ASP PHE THR ILE SEQRES 21 A 413 LYS GLN ASP ASP GLY ALA LEU PRO GLN ASN LEU TYR ARG SEQRES 22 A 413 ALA ASP ILE VAL LEU ALA GLY VAL SER ARG THR GLY LYS SEQRES 23 A 413 THR PRO LEU SER ILE TYR LEU ALA GLN LYS GLY TYR LYS SEQRES 24 A 413 VAL ALA ASN VAL PRO ILE VAL MET GLY VAL ASP LEU PRO SEQRES 25 A 413 LYS SER LEU PHE GLU ILE ASN GLN ASP LYS VAL PHE GLY SEQRES 26 A 413 LEU THR ILE ASN PRO ALA ILE LEU GLN ALA ILE ARG LYS SEQRES 27 A 413 THR ARG ALA LYS THR LEU GLY PHE ASP GLY ARG GLN SER SEQRES 28 A 413 ASN TYR ALA GLU MET ASP HIS VAL ARG GLN GLU LEU VAL SEQRES 29 A 413 HIS ALA ASN GLN ILE PHE ALA GLN ASN PRO SER TRP PRO SEQRES 30 A 413 VAL ILE ALA VAL THR GLY LYS ALA ILE GLU GLU THR ALA SEQRES 31 A 413 ALA VAL ILE LEU GLY ILE LEU HIS ASP ARG LYS GLN LYS SEQRES 32 A 413 CYS SER MET PRO ARG ILE SER LYS ARG TYR HET AMP A 501 23 HET MG A 502 1 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 MG MG 2+ FORMUL 4 HOH *32(H2 O) HELIX 1 AA1 GLY A 148 GLY A 160 1 13 HELIX 2 AA2 PHE A 162 ASP A 168 1 7 HELIX 3 AA3 ASP A 183 GLY A 198 1 16 HELIX 4 AA4 ASP A 207 GLY A 222 1 16 HELIX 5 AA5 LEU A 229 GLY A 241 1 13 HELIX 6 AA6 SER A 259 LYS A 274 1 16 HELIX 7 AA7 ALA A 279 ALA A 287 1 9 HELIX 8 AA8 GLY A 298 GLY A 310 1 13 HELIX 9 AA9 LYS A 326 ILE A 331 1 6 HELIX 10 AB1 ASP A 370 ASN A 386 1 17 HELIX 11 AB2 ALA A 398 GLN A 415 1 18 SHEET 1 AA1 4 VAL A 173 PHE A 178 0 SHEET 2 AA1 4 LYS A 138 SER A 144 1 N ILE A 142 O HIS A 176 SHEET 3 AA1 4 ALA A 199 THR A 204 1 O LEU A 200 N TYR A 141 SHEET 4 AA1 4 CYS A 225 ASP A 227 1 O THR A 226 N VAL A 201 SHEET 1 AA2 4 VAL A 313 PRO A 317 0 SHEET 2 AA2 4 ILE A 289 GLY A 293 1 N LEU A 291 O VAL A 316 SHEET 3 AA2 4 VAL A 336 THR A 340 1 O PHE A 337 N VAL A 290 SHEET 4 AA2 4 VAL A 391 ALA A 393 1 O ILE A 392 N GLY A 338 SSBOND 1 CYS A 128 CYS A 417 1555 4556 2.04 SSBOND 2 CYS A 165 CYS A 171 1555 1555 2.04 LINK O1P AMP A 501 MG MG A 502 1555 1555 2.92 LINK O3P AMP A 501 MG MG A 502 1555 1555 2.97 LINK O5' AMP A 501 MG MG A 502 1555 1555 2.59 SITE 1 AC1 16 SER A 144 ASP A 145 GLY A 146 THR A 147 SITE 2 AC1 16 GLY A 148 TRP A 149 THR A 150 ALA A 157 SITE 3 AC1 16 GLY A 160 GLN A 161 GLU A 163 THR A 204 SITE 4 AC1 16 ILE A 247 PRO A 248 ARG A 249 MG A 502 SITE 1 AC2 7 SER A 144 GLY A 148 TRP A 149 THR A 150 SITE 2 AC2 7 ALA A 151 THR A 204 AMP A 501 CRYST1 175.342 175.342 175.342 90.00 90.00 90.00 P 4 3 2 24 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 0.005703 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005703 0.00000