HEADER PLANT PROTEIN 12-JAN-20 6LPW TITLE STRUCTURE OF SPERMIDINE DISINAPOYL TRANSFERASES(SDT) FROM ARABIDOPSIS TITLE 2 THALIANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERMIDINE SINAPOYL-COA ACYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SPERMIDINE DISINAPOYL TRANSFERASE; COMPND 5 EC: 2.3.1.248; COMPND 6 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: SDT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BAHD TRANSFERASE, PHENOLAMIDES, SPERMIDINE, PUTRESCINE, MULTISITE- KEYWDS 2 ACYLATION, MOLECULAR MECHANISM, SEQUENCE SIMILARITY NETWORK, PLANT KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.WANG,P.ZHANG REVDAT 3 29-NOV-23 6LPW 1 REMARK REVDAT 2 17-FEB-21 6LPW 1 JRNL REVDAT 1 13-JAN-21 6LPW 0 JRNL AUTH C.WANG,J.LI,M.MA,Z.LIN,W.HU,W.LIN,P.ZHANG JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO TWO BAHD JRNL TITL 2 ACYLTRANSFERASES ( AT SHT AND AT SDT) INVOLVED IN JRNL TITL 3 PHENOLAMIDE BIOSYNTHESIS. JRNL REF FRONT PLANT SCI V. 11 10118 2020 JRNL REFN ESSN 1664-462X JRNL PMID 33519864 JRNL DOI 10.3389/FPLS.2020.610118 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 32617 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1661 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 5.4935 - 5.4935 0.99 2838 171 0.2108 0.2364 REMARK 3 2 5.4935 - 4.3613 1.00 2748 142 0.1834 0.2024 REMARK 3 3 4.3613 - 3.8102 0.99 2686 149 0.1762 0.2410 REMARK 3 4 3.8102 - 3.4620 0.99 2701 129 0.1924 0.2111 REMARK 3 5 3.4620 - 3.2139 0.99 2651 126 0.2019 0.2427 REMARK 3 6 3.2139 - 3.0244 0.96 2575 147 0.2127 0.2658 REMARK 3 7 3.0244 - 2.8730 0.94 2500 143 0.2181 0.3010 REMARK 3 8 2.8730 - 2.7479 0.93 2492 133 0.2205 0.2692 REMARK 3 9 2.7479 - 2.6422 0.93 2485 133 0.2124 0.2869 REMARK 3 10 2.6422 - 2.5510 0.93 2465 133 0.2099 0.2726 REMARK 3 11 2.5510 - 2.4712 0.92 2449 136 0.2145 0.2941 REMARK 3 12 2.4712 - 2.4100 0.89 2366 119 0.2167 0.2886 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.44 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LPW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300015257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 500K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32701 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4G0B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES (PH 6.5), 25% W/V PEG 4000 REMARK 280 AT 20 C, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 30.49450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.70550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.53100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.70550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.49450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.53100 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 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: 2720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 152.47250 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 67.70550 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 PRO A 2 REMARK 465 ILE A 3 REMARK 465 HIS A 4 REMARK 465 ILE A 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 ILE A 9 REMARK 465 VAL A 58 REMARK 465 ALA A 59 REMARK 465 ASP A 60 REMARK 465 ASP A 61 REMARK 465 ASP A 62 REMARK 465 GLY A 104 REMARK 465 LEU A 366 REMARK 465 THR A 367 REMARK 465 ILE A 368 REMARK 465 LYS A 369 REMARK 465 GLY A 370 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 ILE B 3 REMARK 465 HIS B 4 REMARK 465 ILE B 5 REMARK 465 GLY B 6 REMARK 465 SER B 7 REMARK 465 SER B 8 REMARK 465 VAL B 58 REMARK 465 ALA B 59 REMARK 465 ASP B 60 REMARK 465 ASP B 61 REMARK 465 ASP B 62 REMARK 465 LEU B 450 REMARK 465 GLU B 451 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 ASN A 57 CG OD1 ND2 REMARK 470 ASN A 63 CG OD1 ND2 REMARK 470 LYS A 208 CG CD CE NZ REMARK 470 ASN A 365 CG OD1 ND2 REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 LYS A 372 CG CD CE NZ REMARK 470 GLU A 451 CG CD OE1 OE2 REMARK 470 ASN B 63 CG OD1 ND2 REMARK 470 ASP B 103 CG OD1 OD2 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 B 603 O HOH B 641 1.92 REMARK 500 O HOH A 531 O HOH B 636 1.97 REMARK 500 O HOH B 601 O HOH B 636 1.99 REMARK 500 O ASP B 395 O HOH B 601 2.00 REMARK 500 O HOH B 637 O HOH B 642 2.01 REMARK 500 O ASP A 395 O HOH A 501 2.04 REMARK 500 OE2 GLU B 210 O HOH B 602 2.06 REMARK 500 O HOH B 627 O HOH B 641 2.10 REMARK 500 OG SER B 389 OE2 GLU B 396 2.11 REMARK 500 O TRP B 381 O HOH B 603 2.14 REMARK 500 NH1 ARG B 89 O ARG B 94 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 396 C PRO B 397 N 0.156 REMARK 500 REMARK 500 REMARK: NULL 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 GLY A 102 N - CA - C ANGL. DEV. = -16.8 DEGREES REMARK 500 LEU A 375 N - CA - CB ANGL. DEV. = 16.3 DEGREES REMARK 500 ASP A 395 CB - CA - C ANGL. DEV. = -35.6 DEGREES REMARK 500 ASP A 395 N - CA - C ANGL. DEV. = 37.1 DEGREES REMARK 500 GLU A 396 N - CA - CB ANGL. DEV. = 32.3 DEGREES REMARK 500 GLU A 396 N - CA - C ANGL. DEV. = -24.8 DEGREES REMARK 500 PHE B 392 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 ASP B 395 CB - CA - C ANGL. DEV. = -31.4 DEGREES REMARK 500 ASP B 395 N - CA - C ANGL. DEV. = 38.5 DEGREES REMARK 500 GLU B 396 N - CA - CB ANGL. DEV. = 31.4 DEGREES REMARK 500 GLU B 396 N - CA - C ANGL. DEV. = -24.0 DEGREES REMARK 500 PRO B 397 C - N - CA ANGL. DEV. = 11.1 DEGREES 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 TYR A 80 51.19 -90.28 REMARK 500 TRP A 200 -77.49 -95.97 REMARK 500 TYR A 256 116.40 -168.05 REMARK 500 SER A 259 -136.57 61.87 REMARK 500 LEU A 375 133.34 -172.09 REMARK 500 ASP A 395 37.89 39.49 REMARK 500 GLU A 396 130.09 107.76 REMARK 500 TYR B 79 -60.32 -98.54 REMARK 500 ARG B 94 16.54 57.87 REMARK 500 ASN B 115 37.73 -87.69 REMARK 500 TRP B 200 -72.54 -92.66 REMARK 500 GLU B 201 45.01 32.93 REMARK 500 ASP B 232 55.76 -100.22 REMARK 500 PHE B 258 45.22 -82.48 REMARK 500 SER B 259 -119.60 60.75 REMARK 500 GLU B 396 119.32 112.80 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 LYS A 208 PRO A 209 -49.89 REMARK 500 PHE B 392 GLY B 393 46.37 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 SPD B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6LPV RELATED DB: PDB DBREF 6LPW A 1 451 UNP O80467 SDT_ARATH 1 451 DBREF 6LPW B 1 451 UNP O80467 SDT_ARATH 1 451 SEQRES 1 A 451 MET PRO ILE HIS ILE GLY SER SER ILE PRO LEU MET VAL SEQRES 2 A 451 GLU LYS MET LEU THR GLU MET VAL LYS PRO SER LYS HIS SEQRES 3 A 451 ILE PRO GLN GLN THR LEU ASN LEU SER THR LEU ASP ASN SEQRES 4 A 451 ASP PRO TYR ASN GLU VAL ILE TYR LYS ALA CYS TYR VAL SEQRES 5 A 451 PHE LYS ALA LYS ASN VAL ALA ASP ASP ASP ASN ARG PRO SEQRES 6 A 451 GLU ALA LEU LEU ARG GLU ALA LEU SER ASP LEU LEU GLY SEQRES 7 A 451 TYR TYR TYR PRO LEU SER GLY SER LEU LYS ARG GLN GLU SEQRES 8 A 451 SER ASP ARG LYS LEU GLN LEU SER CYS GLY GLY ASP GLY SEQRES 9 A 451 GLY GLY VAL PRO PHE THR VAL ALA THR ALA ASN VAL GLU SEQRES 10 A 451 LEU SER SER LEU LYS ASN LEU GLU ASN ILE ASP SER ASP SEQRES 11 A 451 THR ALA LEU ASN PHE LEU PRO VAL LEU HIS VAL ASP ILE SEQRES 12 A 451 ASP GLY TYR ARG PRO PHE ALA LEU GLN VAL THR LYS PHE SEQRES 13 A 451 GLU CYS GLY GLY PHE ILE LEU GLY MET ALA MET SER HIS SEQRES 14 A 451 ALA MET CYS ASP GLY TYR GLY GLU GLY HIS ILE MET CYS SEQRES 15 A 451 ALA LEU THR ASP LEU ALA GLY GLY LYS LYS LYS PRO MET SEQRES 16 A 451 VAL THR PRO ILE TRP GLU ARG GLU ARG LEU VAL GLY LYS SEQRES 17 A 451 PRO GLU ASP ASP GLN PRO PRO PHE VAL PRO GLY ASP ASP SEQRES 18 A 451 THR ALA ALA SER PRO TYR LEU PRO THR ASP ASP TRP VAL SEQRES 19 A 451 THR GLU LYS ILE THR ILE ARG ALA ASP SER ILE ARG ARG SEQRES 20 A 451 LEU LYS GLU ALA THR LEU LYS GLU TYR ASP PHE SER ASN SEQRES 21 A 451 GLU THR ILE THR THR PHE GLU VAL ILE GLY ALA TYR LEU SEQRES 22 A 451 TRP LYS SER ARG VAL LYS ALA LEU ASN LEU ASP ARG ASP SEQRES 23 A 451 GLY VAL THR VAL LEU GLY LEU SER VAL GLY ILE ARG ASN SEQRES 24 A 451 VAL VAL ASP PRO PRO LEU PRO ASP GLY TYR TYR GLY ASN SEQRES 25 A 451 ALA TYR ILE ASP MET TYR VAL PRO LEU THR ALA ARG GLU SEQRES 26 A 451 VAL GLU GLU PHE THR ILE SER ASP ILE VAL LYS LEU ILE SEQRES 27 A 451 LYS GLU ALA LYS ARG ASN ALA HIS ASP LYS ASP TYR LEU SEQRES 28 A 451 GLN GLU GLU LEU ALA ASN THR GLU LYS ILE ILE LYS MET SEQRES 29 A 451 ASN LEU THR ILE LYS GLY LYS LYS ASP GLY LEU PHE CYS SEQRES 30 A 451 LEU THR ASP TRP ARG ASN ILE GLY ILE PHE GLY SER MET SEQRES 31 A 451 ASP PHE GLY TRP ASP GLU PRO VAL ASN ILE VAL PRO VAL SEQRES 32 A 451 VAL PRO SER GLU THR ALA ARG THR VAL ASN MET PHE MET SEQRES 33 A 451 ARG PRO SER ARG LEU GLU SER ASP MET VAL GLY GLY VAL SEQRES 34 A 451 GLN ILE VAL VAL THR LEU PRO ARG ILE ALA MET VAL LYS SEQRES 35 A 451 PHE LYS GLU GLU MET GLU ALA LEU GLU SEQRES 1 B 451 MET PRO ILE HIS ILE GLY SER SER ILE PRO LEU MET VAL SEQRES 2 B 451 GLU LYS MET LEU THR GLU MET VAL LYS PRO SER LYS HIS SEQRES 3 B 451 ILE PRO GLN GLN THR LEU ASN LEU SER THR LEU ASP ASN SEQRES 4 B 451 ASP PRO TYR ASN GLU VAL ILE TYR LYS ALA CYS TYR VAL SEQRES 5 B 451 PHE LYS ALA LYS ASN VAL ALA ASP ASP ASP ASN ARG PRO SEQRES 6 B 451 GLU ALA LEU LEU ARG GLU ALA LEU SER ASP LEU LEU GLY SEQRES 7 B 451 TYR TYR TYR PRO LEU SER GLY SER LEU LYS ARG GLN GLU SEQRES 8 B 451 SER ASP ARG LYS LEU GLN LEU SER CYS GLY GLY ASP GLY SEQRES 9 B 451 GLY GLY VAL PRO PHE THR VAL ALA THR ALA ASN VAL GLU SEQRES 10 B 451 LEU SER SER LEU LYS ASN LEU GLU ASN ILE ASP SER ASP SEQRES 11 B 451 THR ALA LEU ASN PHE LEU PRO VAL LEU HIS VAL ASP ILE SEQRES 12 B 451 ASP GLY TYR ARG PRO PHE ALA LEU GLN VAL THR LYS PHE SEQRES 13 B 451 GLU CYS GLY GLY PHE ILE LEU GLY MET ALA MET SER HIS SEQRES 14 B 451 ALA MET CYS ASP GLY TYR GLY GLU GLY HIS ILE MET CYS SEQRES 15 B 451 ALA LEU THR ASP LEU ALA GLY GLY LYS LYS LYS PRO MET SEQRES 16 B 451 VAL THR PRO ILE TRP GLU ARG GLU ARG LEU VAL GLY LYS SEQRES 17 B 451 PRO GLU ASP ASP GLN PRO PRO PHE VAL PRO GLY ASP ASP SEQRES 18 B 451 THR ALA ALA SER PRO TYR LEU PRO THR ASP ASP TRP VAL SEQRES 19 B 451 THR GLU LYS ILE THR ILE ARG ALA ASP SER ILE ARG ARG SEQRES 20 B 451 LEU LYS GLU ALA THR LEU LYS GLU TYR ASP PHE SER ASN SEQRES 21 B 451 GLU THR ILE THR THR PHE GLU VAL ILE GLY ALA TYR LEU SEQRES 22 B 451 TRP LYS SER ARG VAL LYS ALA LEU ASN LEU ASP ARG ASP SEQRES 23 B 451 GLY VAL THR VAL LEU GLY LEU SER VAL GLY ILE ARG ASN SEQRES 24 B 451 VAL VAL ASP PRO PRO LEU PRO ASP GLY TYR TYR GLY ASN SEQRES 25 B 451 ALA TYR ILE ASP MET TYR VAL PRO LEU THR ALA ARG GLU SEQRES 26 B 451 VAL GLU GLU PHE THR ILE SER ASP ILE VAL LYS LEU ILE SEQRES 27 B 451 LYS GLU ALA LYS ARG ASN ALA HIS ASP LYS ASP TYR LEU SEQRES 28 B 451 GLN GLU GLU LEU ALA ASN THR GLU LYS ILE ILE LYS MET SEQRES 29 B 451 ASN LEU THR ILE LYS GLY LYS LYS ASP GLY LEU PHE CYS SEQRES 30 B 451 LEU THR ASP TRP ARG ASN ILE GLY ILE PHE GLY SER MET SEQRES 31 B 451 ASP PHE GLY TRP ASP GLU PRO VAL ASN ILE VAL PRO VAL SEQRES 32 B 451 VAL PRO SER GLU THR ALA ARG THR VAL ASN MET PHE MET SEQRES 33 B 451 ARG PRO SER ARG LEU GLU SER ASP MET VAL GLY GLY VAL SEQRES 34 B 451 GLN ILE VAL VAL THR LEU PRO ARG ILE ALA MET VAL LYS SEQRES 35 B 451 PHE LYS GLU GLU MET GLU ALA LEU GLU HET SPD B 501 10 HETNAM SPD SPERMIDINE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 3 SPD C7 H19 N3 FORMUL 4 HOH *124(H2 O) HELIX 1 AA1 SER A 35 ASP A 40 1 6 HELIX 2 AA2 PRO A 41 GLU A 44 5 4 HELIX 3 AA3 ARG A 64 TYR A 80 1 17 HELIX 4 AA4 TYR A 81 GLY A 85 5 5 HELIX 5 AA5 GLU A 117 GLU A 125 5 9 HELIX 6 AA6 ASP A 128 LEU A 133 1 6 HELIX 7 AA7 ASN A 134 LEU A 136 5 3 HELIX 8 AA8 ASP A 173 GLY A 189 1 17 HELIX 9 AA9 GLU A 201 VAL A 206 5 6 HELIX 10 AB1 ARG A 241 TYR A 256 1 16 HELIX 11 AB2 THR A 264 ASN A 282 1 19 HELIX 12 AB3 ALA A 323 PHE A 329 1 7 HELIX 13 AB4 THR A 330 HIS A 346 1 17 HELIX 14 AB5 ASP A 347 ASN A 365 1 19 HELIX 15 AB6 ARG A 382 ILE A 386 5 5 HELIX 16 AB7 GLU A 422 VAL A 426 5 5 HELIX 17 AB8 ARG A 437 ALA A 449 1 13 HELIX 18 AB9 SER B 35 ASP B 40 1 6 HELIX 19 AC1 PRO B 41 GLU B 44 5 4 HELIX 20 AC2 ARG B 64 LEU B 77 1 14 HELIX 21 AC3 GLY B 78 TYR B 79 5 2 HELIX 22 AC4 TYR B 80 GLY B 85 5 6 HELIX 23 AC5 GLU B 117 GLU B 125 5 9 HELIX 24 AC6 ASP B 128 LEU B 133 1 6 HELIX 25 AC7 ASN B 134 LEU B 136 5 3 HELIX 26 AC8 ASP B 173 GLY B 189 1 17 HELIX 27 AC9 GLU B 201 VAL B 206 5 6 HELIX 28 AD1 ARG B 241 LYS B 254 1 14 HELIX 29 AD2 THR B 264 ASN B 282 1 19 HELIX 30 AD3 ALA B 323 PHE B 329 1 7 HELIX 31 AD4 THR B 330 HIS B 346 1 17 HELIX 32 AD5 ASP B 347 ASN B 365 1 19 HELIX 33 AD6 THR B 408 ARG B 410 5 3 HELIX 34 AD7 GLU B 422 VAL B 426 5 5 HELIX 35 AD8 ARG B 437 ALA B 449 1 13 SHEET 1 AA1 6 VAL A 13 VAL A 21 0 SHEET 2 AA1 6 VAL A 107 ALA A 114 -1 O VAL A 111 N MET A 16 SHEET 3 AA1 6 PHE A 149 LYS A 155 1 O LYS A 155 N ALA A 112 SHEET 4 AA1 6 PHE A 161 SER A 168 -1 O GLY A 164 N GLN A 152 SHEET 5 AA1 6 ILE A 46 PHE A 53 -1 N TYR A 51 O LEU A 163 SHEET 6 AA1 6 ASN A 399 VAL A 403 -1 O VAL A 403 N LYS A 48 SHEET 1 AA2 3 GLN A 30 ASN A 33 0 SHEET 2 AA2 3 LEU A 96 CYS A 100 -1 O LEU A 98 N LEU A 32 SHEET 3 AA2 3 SER A 86 ARG A 89 -1 N LYS A 88 O GLN A 97 SHEET 1 AA3 2 VAL A 141 ASP A 142 0 SHEET 2 AA3 2 GLY A 145 TYR A 146 -1 O GLY A 145 N ASP A 142 SHEET 1 AA4 6 TRP A 233 ILE A 240 0 SHEET 2 AA4 6 VAL A 429 PRO A 436 -1 O LEU A 435 N VAL A 234 SHEET 3 AA4 6 VAL A 412 MET A 416 -1 N MET A 416 O GLN A 430 SHEET 4 AA4 6 PHE A 376 ASP A 380 1 N THR A 379 O PHE A 415 SHEET 5 AA4 6 VAL A 288 GLY A 296 1 N GLY A 292 O PHE A 376 SHEET 6 AA4 6 TYR A 314 THR A 322 -1 O LEU A 321 N THR A 289 SHEET 1 AA5 6 VAL B 13 VAL B 21 0 SHEET 2 AA5 6 VAL B 107 ALA B 114 -1 O VAL B 111 N MET B 16 SHEET 3 AA5 6 PHE B 149 LYS B 155 1 O LYS B 155 N ALA B 112 SHEET 4 AA5 6 PHE B 161 SER B 168 -1 O GLY B 164 N GLN B 152 SHEET 5 AA5 6 ILE B 46 PHE B 53 -1 N TYR B 51 O LEU B 163 SHEET 6 AA5 6 ASN B 399 VAL B 403 -1 O VAL B 401 N CYS B 50 SHEET 1 AA6 3 GLN B 30 ASN B 33 0 SHEET 2 AA6 3 LEU B 96 CYS B 100 -1 O LEU B 98 N LEU B 32 SHEET 3 AA6 3 SER B 86 ARG B 89 -1 N LYS B 88 O GLN B 97 SHEET 1 AA7 2 VAL B 141 ASP B 142 0 SHEET 2 AA7 2 GLY B 145 TYR B 146 -1 O GLY B 145 N ASP B 142 SHEET 1 AA8 6 TRP B 233 ILE B 240 0 SHEET 2 AA8 6 VAL B 429 PRO B 436 -1 O ILE B 431 N ILE B 238 SHEET 3 AA8 6 VAL B 412 MET B 416 -1 N MET B 416 O GLN B 430 SHEET 4 AA8 6 LEU B 375 ASP B 380 1 N THR B 379 O PHE B 415 SHEET 5 AA8 6 VAL B 288 GLY B 296 1 N VAL B 290 O PHE B 376 SHEET 6 AA8 6 TYR B 314 THR B 322 -1 O MET B 317 N LEU B 293 CISPEP 1 LEU A 228 PRO A 229 0 3.00 CISPEP 2 ASP A 302 PRO A 303 0 -4.76 CISPEP 3 ASP A 373 GLY A 374 0 17.68 CISPEP 4 ILE B 9 PRO B 10 0 -0.81 CISPEP 5 LEU B 228 PRO B 229 0 -0.89 CISPEP 6 ASP B 302 PRO B 303 0 -1.16 SITE 1 AC1 12 TYR B 42 TYR B 47 HIS B 169 GLY B 292 SITE 2 AC1 12 LEU B 293 SER B 294 TYR B 314 ASP B 316 SITE 3 AC1 12 CYS B 377 LEU B 378 HOH B 604 HOH B 633 CRYST1 60.989 103.062 135.411 90.00 90.00 90.00 P 21 21 21 8 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 0.016396 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007385 0.00000