HEADER TRANSFERASE 27-FEB-17 5N9Q TITLE STRUCTURE OF A. THALIANA RCD1(468-567) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INACTIVE POLY [ADP-RIBOSE] POLYMERASE RCD1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN RADICAL-INDUCED CELL DEATH 1; COMPND 5 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: RCD1, ATP8, CEO1, AT1G32230, F3C3.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELICAL BUNDLE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR H.TOSSAVAINEN,M.HELLMAN,J.VAINONEN,J.KANGASJARVI,P.PERMI REVDAT 4 14-JUN-23 5N9Q 1 REMARK REVDAT 3 25-SEP-19 5N9Q 1 JRNL REMARK REVDAT 2 08-MAY-19 5N9Q 1 REMARK REVDAT 1 14-MAR-18 5N9Q 0 JRNL AUTH A.SHAPIGUZOV,J.P.VAINONEN,K.HUNTER,H.TOSSAVAINEN,A.TIWARI, JRNL AUTH 2 S.JARVI,M.HELLMAN,F.AARABI,S.ALSEEKH,B.WYBOUW, JRNL AUTH 3 K.VAN DER KELEN,L.NIKKANEN,J.KRASENSKY-WRZACZEK,N.SIPARI, JRNL AUTH 4 M.KEINANEN,E.TYYSTJARVI,E.RINTAMAKI,B.DE RYBEL,J.SALOJARVI, JRNL AUTH 5 F.VAN BREUSEGEM,A.R.FERNIE,M.BROSCHE,P.PERMI,E.M.ARO, JRNL AUTH 6 M.WRZACZEK,J.KANGASJARVI JRNL TITL ARABIDOPSIS RCD1 COORDINATES CHLOROPLAST AND MITOCHONDRIAL JRNL TITL 2 FUNCTIONS THROUGH INTERACTION WITH ANAC TRANSCRIPTION JRNL TITL 3 FACTORS. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 30767893 JRNL DOI 10.7554/ELIFE.43284 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5N9Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003532. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.11 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-13C; U-15N] RCD1, 20 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D H(CCO)NH; 3D C(CO) REMARK 210 NH; 3D HCCMHM; 3D IHACANCO; 3D REMARK 210 HACACON; 3D HACACONCAHA; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 12460 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 ARG A 548 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 ARG A 551 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 488 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 551 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 537 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 551 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ARG A 488 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 ARG A 537 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ARG A 548 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 ARG A 560 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 580 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 537 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 560 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 548 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 537 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 560 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 488 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG A 548 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 551 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 560 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 580 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 9 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 548 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 551 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 560 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 ARG A 580 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG A 537 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 10 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 548 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 551 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG A 488 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 11 ARG A 537 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 11 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 548 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 537 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 67 ANGLE DEVIATIONS. 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 1 SER A 463 70.16 57.61 REMARK 500 1 PHE A 466 90.21 54.68 REMARK 500 1 LYS A 475 -16.52 -145.97 REMARK 500 1 MET A 508 49.77 -155.18 REMARK 500 1 HIS A 582 -3.09 -154.74 REMARK 500 2 LYS A 475 48.58 -77.03 REMARK 500 2 ASP A 476 41.26 -79.10 REMARK 500 2 GLN A 485 -31.16 -136.67 REMARK 500 2 SER A 492 109.84 -57.29 REMARK 500 2 SER A 499 -29.83 59.50 REMARK 500 2 THR A 501 -22.18 -147.85 REMARK 500 2 LYS A 504 -133.83 -82.06 REMARK 500 2 PRO A 506 42.55 -77.79 REMARK 500 2 TRP A 507 33.16 -73.05 REMARK 500 2 LYS A 539 17.17 56.74 REMARK 500 2 ASN A 568 -74.08 -119.26 REMARK 500 2 GLN A 569 155.10 57.89 REMARK 500 2 PRO A 576 46.25 -78.77 REMARK 500 3 ASP A 476 37.55 -75.53 REMARK 500 3 THR A 500 10.64 55.56 REMARK 500 3 PRO A 509 -169.66 -65.23 REMARK 500 3 PHE A 510 161.28 67.29 REMARK 500 3 PRO A 511 7.41 -64.36 REMARK 500 3 ASN A 568 -70.43 -130.81 REMARK 500 3 GLN A 569 162.64 55.45 REMARK 500 3 LYS A 571 29.58 -69.48 REMARK 500 3 ILE A 579 114.34 51.99 REMARK 500 4 PRO A 503 -5.85 -55.45 REMARK 500 4 LYS A 504 153.43 -48.50 REMARK 500 4 PRO A 506 95.29 -62.50 REMARK 500 4 PRO A 511 -9.54 -59.06 REMARK 500 5 SER A 463 72.29 54.08 REMARK 500 5 PHE A 466 -32.16 -149.73 REMARK 500 5 VAL A 469 -9.00 57.36 REMARK 500 5 ASP A 476 40.13 -88.13 REMARK 500 5 SER A 498 -16.41 -149.58 REMARK 500 5 ARG A 502 150.13 62.79 REMARK 500 5 MET A 508 -23.29 -160.13 REMARK 500 5 PRO A 511 -5.59 -58.71 REMARK 500 5 LYS A 539 18.69 58.20 REMARK 500 5 PRO A 576 40.22 -74.15 REMARK 500 5 ILE A 579 88.79 61.67 REMARK 500 6 SER A 463 73.67 44.68 REMARK 500 6 MET A 467 14.73 54.04 REMARK 500 6 SER A 483 -43.20 61.12 REMARK 500 6 SER A 499 47.55 -71.92 REMARK 500 6 ARG A 502 68.67 -117.63 REMARK 500 6 LYS A 504 3.03 57.43 REMARK 500 6 MET A 508 -11.64 -158.69 REMARK 500 6 PHE A 510 -40.78 -161.30 REMARK 500 REMARK 500 THIS ENTRY HAS 100 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 508 PRO A 509 6 -69.11 REMARK 500 PRO A 509 PHE A 510 6 149.34 REMARK 500 GLU A 482 SER A 483 8 141.97 REMARK 500 MET A 508 PRO A 509 10 149.16 REMARK 500 MET A 508 PRO A 509 15 149.78 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 1 ARG A 502 0.11 SIDE CHAIN REMARK 500 9 ARG A 537 0.09 SIDE CHAIN REMARK 500 12 TYR A 533 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27034 RELATED DB: BMRB DBREF 5N9Q A 468 589 UNP Q8RY59 RCD1_ARATH 468 589 SEQADV 5N9Q GLY A 462 UNP Q8RY59 EXPRESSION TAG SEQADV 5N9Q SER A 463 UNP Q8RY59 EXPRESSION TAG SEQADV 5N9Q PRO A 464 UNP Q8RY59 EXPRESSION TAG SEQADV 5N9Q GLU A 465 UNP Q8RY59 EXPRESSION TAG SEQADV 5N9Q PHE A 466 UNP Q8RY59 EXPRESSION TAG SEQADV 5N9Q MET A 467 UNP Q8RY59 EXPRESSION TAG SEQRES 1 A 128 GLY SER PRO GLU PHE MET GLY VAL THR LEU GLU GLY PRO SEQRES 2 A 128 LYS ASP LEU PRO PRO GLN LEU GLU SER ASN GLN GLY ALA SEQRES 3 A 128 ARG GLY SER GLY SER ALA ASN SER VAL GLY SER SER THR SEQRES 4 A 128 THR ARG PRO LYS SER PRO TRP MET PRO PHE PRO THR LEU SEQRES 5 A 128 PHE ALA ALA ILE SER HIS LYS VAL ALA GLU ASN ASP MET SEQRES 6 A 128 LEU LEU ILE ASN ALA ASP TYR GLN GLN LEU ARG ASP LYS SEQRES 7 A 128 LYS MET THR ARG ALA GLU PHE VAL ARG LYS LEU ARG VAL SEQRES 8 A 128 ILE VAL GLY ASP ASP LEU LEU ARG SER THR ILE THR THR SEQRES 9 A 128 LEU GLN ASN GLN PRO LYS SER LYS GLU ILE PRO GLY SER SEQRES 10 A 128 ILE ARG ASP HIS GLU GLU GLY ALA GLY GLY LEU HELIX 1 AA1 PRO A 509 SER A 518 1 10 HELIX 2 AA2 ALA A 522 ASP A 538 1 17 HELIX 3 AA3 THR A 542 ARG A 551 1 10 HELIX 4 AA4 GLY A 555 GLN A 567 1 13 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1