HEADER BIOSYNTHETIC PROTEIN 18-AUG-15 5D9R TITLE CRYSTAL STRUCTURE OF A CONSERVED DOMAIN IN THE INTERMEMBRANE SPACE TITLE 2 REGION OF THE PLASTID DIVISION PROTEIN ARC6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, COMPND 3 CHLOROPLASTIC; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: ARC6, AT5G42480, MDH9.18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS PLASTID DIVISION MACHINERY, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.RADHAKRISHNAN,N.KUMAR,C.-C.SU,T.-H.CHOU,E.YU REVDAT 4 06-MAR-24 5D9R 1 REMARK REVDAT 3 22-NOV-17 5D9R 1 JRNL REMARK REVDAT 2 10-FEB-16 5D9R 1 JRNL REVDAT 1 11-NOV-15 5D9R 0 JRNL AUTH N.KUMAR,A.RADHAKRISHNAN,C.C.SU,K.W.OSTERYOUNG,E.W.YU JRNL TITL CRYSTAL STRUCTURE OF A CONSERVED DOMAIN IN THE INTERMEMBRANE JRNL TITL 2 SPACE REGION OF THE PLASTID DIVISION PROTEIN ARC6. JRNL REF PROTEIN SCI. V. 25 523 2016 JRNL REFN ESSN 1469-896X JRNL PMID 26452626 JRNL DOI 10.1002/PRO.2825 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 636 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1039 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.86 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5D9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12651 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 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: NULL REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, MAGNESIUM SULFATE, TRI-SODIUM REMARK 280 CITRATE, ISOPROPANOL, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 30.77533 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 61.55067 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 61.55067 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 30.77533 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 HIS A 618 REMARK 465 HIS A 619 REMARK 465 HIS A 620 REMARK 465 HIS A 621 REMARK 465 HIS A 622 REMARK 465 HIS A 623 REMARK 465 HIS A 624 REMARK 465 HIS A 625 REMARK 465 GLY A 626 REMARK 465 GLY A 627 REMARK 465 LEU A 628 REMARK 465 VAL A 629 REMARK 465 PRO A 630 REMARK 465 ARG A 631 REMARK 465 GLY A 632 REMARK 465 SER A 633 REMARK 465 HIS A 634 REMARK 465 GLY A 635 REMARK 465 TYR A 636 REMARK 465 PHE A 637 REMARK 465 LEU A 638 REMARK 465 LYS A 639 REMARK 465 SER A 640 REMARK 465 SER A 641 REMARK 465 SER A 642 REMARK 465 SER A 643 REMARK 465 PHE A 644 REMARK 465 GLN A 645 REMARK 465 ARG A 646 REMARK 465 LYS A 647 REMARK 465 ASP A 648 REMARK 465 MET A 649 REMARK 465 VAL A 650 REMARK 465 SER A 651 REMARK 465 SER A 652 REMARK 465 MET A 653 REMARK 465 GLU A 654 REMARK 465 SER A 655 REMARK 465 ASP A 656 REMARK 465 VAL A 657 REMARK 465 ALA A 658 REMARK 465 THR A 659 REMARK 465 ILE A 660 REMARK 465 GLY A 661 REMARK 465 SER A 662 REMARK 465 VAL A 663 REMARK 465 ARG A 664 REMARK 465 ALA A 665 REMARK 465 ASP A 666 REMARK 465 ASP A 667 REMARK 465 ALA A 800 REMARK 465 SER A 801 DBREF 5D9R A 636 801 UNP Q9FIG9 ARC6_ARATH 636 801 SEQADV 5D9R HIS A 618 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 619 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 620 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 621 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 622 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 623 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 624 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 625 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R GLY A 626 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R GLY A 627 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R LEU A 628 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R VAL A 629 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R PRO A 630 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R ARG A 631 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R GLY A 632 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R SER A 633 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R HIS A 634 UNP Q9FIG9 EXPRESSION TAG SEQADV 5D9R GLY A 635 UNP Q9FIG9 EXPRESSION TAG SEQRES 1 A 184 HIS HIS HIS HIS HIS HIS HIS HIS GLY GLY LEU VAL PRO SEQRES 2 A 184 ARG GLY SER HIS GLY TYR PHE LEU LYS SER SER SER SER SEQRES 3 A 184 PHE GLN ARG LYS ASP MET VAL SER SER MET GLU SER ASP SEQRES 4 A 184 VAL ALA THR ILE GLY SER VAL ARG ALA ASP ASP SER GLU SEQRES 5 A 184 ALA LEU PRO ARG MET ASP ALA ARG THR ALA GLU ASN ILE SEQRES 6 A 184 VAL SER LYS TRP GLN LYS ILE LYS SER LEU ALA PHE GLY SEQRES 7 A 184 PRO ASP HIS ARG ILE GLU MET LEU PRO GLU VAL LEU ASP SEQRES 8 A 184 GLY ARG MET LEU LYS ILE TRP THR ASP ARG ALA ALA GLU SEQRES 9 A 184 THR ALA GLN LEU GLY LEU VAL TYR ASP TYR THR LEU LEU SEQRES 10 A 184 LYS LEU SER VAL ASP SER VAL THR VAL SER ALA ASP GLY SEQRES 11 A 184 THR ARG ALA LEU VAL GLU ALA THR LEU GLU GLU SER ALA SEQRES 12 A 184 CYS LEU SER ASP LEU VAL HIS PRO GLU ASN ASN ALA THR SEQRES 13 A 184 ASP VAL ARG THR TYR THR THR ARG TYR GLU VAL PHE TRP SEQRES 14 A 184 SER LYS SER GLY TRP LYS ILE THR GLU GLY SER VAL LEU SEQRES 15 A 184 ALA SER FORMUL 2 HOH *75(H2 O) HELIX 1 AA1 ASP A 675 GLY A 695 1 21 HELIX 2 AA2 ARG A 699 VAL A 706 5 8 HELIX 3 AA3 ASP A 708 GLY A 726 1 19 HELIX 4 AA4 HIS A 767 ASN A 771 5 5 SHEET 1 AA1 4 LEU A 727 VAL A 743 0 SHEET 2 AA1 4 ARG A 749 ASP A 764 -1 O GLU A 757 N LEU A 734 SHEET 3 AA1 4 ALA A 772 SER A 787 -1 O TYR A 782 N VAL A 752 SHEET 4 AA1 4 GLY A 790 VAL A 798 -1 O GLU A 795 N GLU A 783 CRYST1 60.339 60.339 92.326 90.00 90.00 120.00 P 31 2 1 6 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 0.016573 0.009568 0.000000 0.00000 SCALE2 0.000000 0.019137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010831 0.00000