HEADER CHAPERONE 23-OCT-21 7VRR TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA HDT1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE HDT1; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: HD-TUINS PROTEIN 1,HISTONE DEACETYLASE 2A; 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: HDT1, HD2A, HDA3, AT3G44750, T32N15.8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS HDAC, HD-TUIN, HDT, HISTONE DEACTYLASE, NUCLEOPLASMIN, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,R.C.BOBDE,D.VASUDEVAN REVDAT 3 29-NOV-23 7VRR 1 REMARK REVDAT 2 14-DEC-22 7VRR 1 JRNL REVDAT 1 21-SEP-22 7VRR 0 JRNL AUTH R.C.BOBDE,A.KUMAR,D.VASUDEVAN JRNL TITL PLANT-SPECIFIC HDT FAMILY HISTONE DEACETYLASES ARE JRNL TITL 2 NUCLEOPLASMINS. JRNL REF PLANT CELL V. 34 4760 2022 JRNL REFN ESSN 1532-298X JRNL PMID 36069647 JRNL DOI 10.1093/PLCELL/KOAC275 REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 2.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 698 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3554 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3670 ; 0.009 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3484 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4965 ; 1.315 ; 1.879 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8079 ; 0.950 ; 2.824 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 443 ; 6.299 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;42.124 ;25.733 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 628 ;15.327 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 561 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4038 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 758 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 96 REMARK 3 ORIGIN FOR THE GROUP (A): 21.1370 75.7490 -5.9420 REMARK 3 T TENSOR REMARK 3 T11: 0.1007 T22: 0.0857 REMARK 3 T33: 0.1858 T12: -0.0540 REMARK 3 T13: -0.0581 T23: 0.1053 REMARK 3 L TENSOR REMARK 3 L11: 5.6462 L22: 6.0354 REMARK 3 L33: 5.3526 L12: 0.4831 REMARK 3 L13: 0.3364 L23: -1.9644 REMARK 3 S TENSOR REMARK 3 S11: -0.0181 S12: 0.1282 S13: 0.4069 REMARK 3 S21: 0.0410 S22: -0.1590 S23: -0.3789 REMARK 3 S31: -0.5111 S32: 0.0089 S33: 0.1771 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 95 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4960 61.0050 -11.5940 REMARK 3 T TENSOR REMARK 3 T11: 0.1552 T22: 0.1264 REMARK 3 T33: 0.0541 T12: -0.0315 REMARK 3 T13: -0.0801 T23: 0.0126 REMARK 3 L TENSOR REMARK 3 L11: 3.6406 L22: 4.9892 REMARK 3 L33: 5.9038 L12: 0.7914 REMARK 3 L13: 1.9148 L23: -1.6519 REMARK 3 S TENSOR REMARK 3 S11: 0.1097 S12: 0.2419 S13: 0.0802 REMARK 3 S21: -0.4983 S22: -0.1556 S23: 0.2784 REMARK 3 S31: 0.3598 S32: -0.2979 S33: 0.0459 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 95 REMARK 3 ORIGIN FOR THE GROUP (A): 30.0920 70.3960 10.6650 REMARK 3 T TENSOR REMARK 3 T11: 0.2646 T22: 0.1261 REMARK 3 T33: 0.3217 T12: -0.1190 REMARK 3 T13: -0.2680 T23: 0.1217 REMARK 3 L TENSOR REMARK 3 L11: 5.2541 L22: 6.7127 REMARK 3 L33: 3.8497 L12: 0.2642 REMARK 3 L13: 0.0504 L23: -0.6676 REMARK 3 S TENSOR REMARK 3 S11: -0.0983 S12: -0.3279 S13: 0.1026 REMARK 3 S21: 0.9439 S22: -0.3120 S23: -0.8205 REMARK 3 S31: -0.2632 S32: 0.4673 S33: 0.4103 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 96 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9990 52.2540 15.3570 REMARK 3 T TENSOR REMARK 3 T11: 0.1996 T22: 0.0750 REMARK 3 T33: 0.0861 T12: -0.0899 REMARK 3 T13: -0.1203 T23: 0.0598 REMARK 3 L TENSOR REMARK 3 L11: 4.7534 L22: 8.5485 REMARK 3 L33: 5.8503 L12: -0.9218 REMARK 3 L13: 2.4346 L23: -1.9905 REMARK 3 S TENSOR REMARK 3 S11: 0.0616 S12: -0.3727 S13: 0.0266 REMARK 3 S21: 0.7427 S22: -0.1809 S23: -0.4602 REMARK 3 S31: -0.0687 S32: -0.0950 S33: 0.1192 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 95 REMARK 3 ORIGIN FOR THE GROUP (A): 11.3720 46.4690 1.5490 REMARK 3 T TENSOR REMARK 3 T11: 0.2405 T22: 0.0790 REMARK 3 T33: 0.0741 T12: -0.1268 REMARK 3 T13: -0.0729 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 4.3988 L22: 6.5539 REMARK 3 L33: 6.3399 L12: 0.1362 REMARK 3 L13: 1.3375 L23: -2.2029 REMARK 3 S TENSOR REMARK 3 S11: 0.1969 S12: 0.1031 S13: -0.1774 REMARK 3 S21: -0.2088 S22: 0.0744 S23: 0.6000 REMARK 3 S31: 0.6245 S32: -0.3573 S33: -0.2713 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7VRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300025265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979470 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10405 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 44.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.63700 REMARK 200 R SYM FOR SHELL (I) : 0.70500 REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 7VMF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MGCL2.6H2O, 0.1M HEPES (PH 7.5), REMARK 280 30% V/V PEG MME 550, VAPOR DIFFUSION, TEMPERATURE 301K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 71.81250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.98050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.98050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.71875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.98050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.98050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.90625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.98050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.98050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 107.71875 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.98050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.98050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.90625 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 71.81250 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 ASN A 36 REMARK 465 LYS A 37 REMARK 465 CYS B 34 REMARK 465 LYS B 35 REMARK 465 ASN B 36 REMARK 465 ASN B 96 REMARK 465 GLU C 19 REMARK 465 GLU C 20 REMARK 465 GLY C 21 REMARK 465 CYS C 34 REMARK 465 LYS C 35 REMARK 465 ASN C 36 REMARK 465 LYS C 37 REMARK 465 LYS C 38 REMARK 465 GLY C 39 REMARK 465 ASN C 96 REMARK 465 CYS D 34 REMARK 465 LYS D 37 REMARK 465 LYS D 38 REMARK 465 GLY D 39 REMARK 465 TRP D 82 REMARK 465 GLY E 39 REMARK 465 GLY E 83 REMARK 465 LYS E 84 REMARK 465 ASN E 96 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 38 CG CD CE NZ REMARK 470 GLU D 40 CG CD OE1 OE2 REMARK 470 PHE D 41 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS E 12 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 O LYS E 38 N GLU E 40 1.51 REMARK 500 O THR D 81 N GLY D 83 2.04 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 LYS A 84 47.52 -105.22 REMARK 500 LYS B 38 145.22 -170.39 REMARK 500 LYS B 84 42.17 -106.42 REMARK 500 ASN C 50 -3.47 73.58 REMARK 500 LYS C 84 44.15 -106.02 REMARK 500 LYS D 84 52.47 -110.13 REMARK 500 GLU E 61 -50.32 76.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7VMF RELATED DB: PDB REMARK 900 RELATED ID: 7VMH RELATED DB: PDB REMARK 900 RELATED ID: 7VMI RELATED DB: PDB DBREF 7VRR A 1 96 UNP Q9FVE6 HDT1_ARATH 1 96 DBREF 7VRR B 1 96 UNP Q9FVE6 HDT1_ARATH 1 96 DBREF 7VRR C 1 96 UNP Q9FVE6 HDT1_ARATH 1 96 DBREF 7VRR D 1 96 UNP Q9FVE6 HDT1_ARATH 1 96 DBREF 7VRR E 1 96 UNP Q9FVE6 HDT1_ARATH 1 96 SEQRES 1 A 96 MET GLU PHE TRP GLY ILE GLU VAL LYS SER GLY LYS PRO SEQRES 2 A 96 VAL THR VAL THR PRO GLU GLU GLY ILE LEU ILE HIS VAL SEQRES 3 A 96 SER GLN ALA SER LEU GLY GLU CYS LYS ASN LYS LYS GLY SEQRES 4 A 96 GLU PHE VAL PRO LEU HIS VAL LYS VAL GLY ASN GLN ASN SEQRES 5 A 96 LEU VAL LEU GLY THR LEU SER THR GLU ASN ILE PRO GLN SEQRES 6 A 96 LEU PHE CYS ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SEQRES 7 A 96 SER HIS THR TRP GLY LYS GLY SER VAL TYR PHE VAL GLY SEQRES 8 A 96 TYR LYS THR PRO ASN SEQRES 1 B 96 MET GLU PHE TRP GLY ILE GLU VAL LYS SER GLY LYS PRO SEQRES 2 B 96 VAL THR VAL THR PRO GLU GLU GLY ILE LEU ILE HIS VAL SEQRES 3 B 96 SER GLN ALA SER LEU GLY GLU CYS LYS ASN LYS LYS GLY SEQRES 4 B 96 GLU PHE VAL PRO LEU HIS VAL LYS VAL GLY ASN GLN ASN SEQRES 5 B 96 LEU VAL LEU GLY THR LEU SER THR GLU ASN ILE PRO GLN SEQRES 6 B 96 LEU PHE CYS ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SEQRES 7 B 96 SER HIS THR TRP GLY LYS GLY SER VAL TYR PHE VAL GLY SEQRES 8 B 96 TYR LYS THR PRO ASN SEQRES 1 C 96 MET GLU PHE TRP GLY ILE GLU VAL LYS SER GLY LYS PRO SEQRES 2 C 96 VAL THR VAL THR PRO GLU GLU GLY ILE LEU ILE HIS VAL SEQRES 3 C 96 SER GLN ALA SER LEU GLY GLU CYS LYS ASN LYS LYS GLY SEQRES 4 C 96 GLU PHE VAL PRO LEU HIS VAL LYS VAL GLY ASN GLN ASN SEQRES 5 C 96 LEU VAL LEU GLY THR LEU SER THR GLU ASN ILE PRO GLN SEQRES 6 C 96 LEU PHE CYS ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SEQRES 7 C 96 SER HIS THR TRP GLY LYS GLY SER VAL TYR PHE VAL GLY SEQRES 8 C 96 TYR LYS THR PRO ASN SEQRES 1 D 96 MET GLU PHE TRP GLY ILE GLU VAL LYS SER GLY LYS PRO SEQRES 2 D 96 VAL THR VAL THR PRO GLU GLU GLY ILE LEU ILE HIS VAL SEQRES 3 D 96 SER GLN ALA SER LEU GLY GLU CYS LYS ASN LYS LYS GLY SEQRES 4 D 96 GLU PHE VAL PRO LEU HIS VAL LYS VAL GLY ASN GLN ASN SEQRES 5 D 96 LEU VAL LEU GLY THR LEU SER THR GLU ASN ILE PRO GLN SEQRES 6 D 96 LEU PHE CYS ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SEQRES 7 D 96 SER HIS THR TRP GLY LYS GLY SER VAL TYR PHE VAL GLY SEQRES 8 D 96 TYR LYS THR PRO ASN SEQRES 1 E 96 MET GLU PHE TRP GLY ILE GLU VAL LYS SER GLY LYS PRO SEQRES 2 E 96 VAL THR VAL THR PRO GLU GLU GLY ILE LEU ILE HIS VAL SEQRES 3 E 96 SER GLN ALA SER LEU GLY GLU CYS LYS ASN LYS LYS GLY SEQRES 4 E 96 GLU PHE VAL PRO LEU HIS VAL LYS VAL GLY ASN GLN ASN SEQRES 5 E 96 LEU VAL LEU GLY THR LEU SER THR GLU ASN ILE PRO GLN SEQRES 6 E 96 LEU PHE CYS ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SEQRES 7 E 96 SER HIS THR TRP GLY LYS GLY SER VAL TYR PHE VAL GLY SEQRES 8 E 96 TYR LYS THR PRO ASN SHEET 1 AA1 4 GLU A 2 LYS A 9 0 SHEET 2 AA1 4 SER A 86 PRO A 95 -1 O GLY A 91 N TRP A 4 SHEET 3 AA1 4 ILE A 22 LEU A 31 -1 N LEU A 23 O THR A 94 SHEET 4 AA1 4 GLN A 65 PHE A 72 -1 O CYS A 68 N SER A 27 SHEET 1 AA2 4 VAL A 14 VAL A 16 0 SHEET 2 AA2 4 PHE A 76 SER A 79 -1 O PHE A 76 N VAL A 16 SHEET 3 AA2 4 PHE A 41 VAL A 48 -1 N HIS A 45 O SER A 79 SHEET 4 AA2 4 GLN A 51 SER A 59 -1 O GLY A 56 N LEU A 44 SHEET 1 AA3 4 GLU B 2 LYS B 9 0 SHEET 2 AA3 4 SER B 86 THR B 94 -1 O GLY B 91 N TRP B 4 SHEET 3 AA3 4 LEU B 23 LEU B 31 -1 N LEU B 23 O THR B 94 SHEET 4 AA3 4 GLN B 65 PHE B 72 -1 O CYS B 68 N SER B 27 SHEET 1 AA4 4 VAL B 14 VAL B 16 0 SHEET 2 AA4 4 PHE B 76 HIS B 80 -1 O PHE B 76 N VAL B 16 SHEET 3 AA4 4 PHE B 41 VAL B 48 -1 N HIS B 45 O SER B 79 SHEET 4 AA4 4 GLN B 51 SER B 59 -1 O GLY B 56 N LEU B 44 SHEET 1 AA5 4 GLU C 2 LYS C 9 0 SHEET 2 AA5 4 SER C 86 THR C 94 -1 O GLY C 91 N TRP C 4 SHEET 3 AA5 4 LEU C 23 LEU C 31 -1 N LEU C 23 O THR C 94 SHEET 4 AA5 4 GLN C 65 PHE C 72 -1 O CYS C 68 N SER C 27 SHEET 1 AA6 4 VAL C 14 VAL C 16 0 SHEET 2 AA6 4 PHE C 76 HIS C 80 -1 O PHE C 76 N VAL C 16 SHEET 3 AA6 4 PHE C 41 VAL C 48 -1 N HIS C 45 O SER C 79 SHEET 4 AA6 4 GLN C 51 SER C 59 -1 O GLY C 56 N LEU C 44 SHEET 1 AA7 4 GLU D 2 LYS D 9 0 SHEET 2 AA7 4 SER D 86 PRO D 95 -1 O GLY D 91 N TRP D 4 SHEET 3 AA7 4 ILE D 22 LEU D 31 -1 N LEU D 23 O THR D 94 SHEET 4 AA7 4 GLN D 65 PHE D 72 -1 O CYS D 68 N SER D 27 SHEET 1 AA8 4 VAL D 14 VAL D 16 0 SHEET 2 AA8 4 PHE D 76 HIS D 80 -1 O PHE D 76 N VAL D 16 SHEET 3 AA8 4 PHE D 41 VAL D 48 -1 N HIS D 45 O SER D 79 SHEET 4 AA8 4 GLN D 51 SER D 59 -1 O LEU D 58 N VAL D 42 SHEET 1 AA9 4 GLU E 2 LYS E 9 0 SHEET 2 AA9 4 SER E 86 THR E 94 -1 O GLY E 91 N TRP E 4 SHEET 3 AA9 4 LEU E 23 LEU E 31 -1 N LEU E 23 O THR E 94 SHEET 4 AA9 4 GLN E 65 PHE E 72 -1 O CYS E 68 N SER E 27 SHEET 1 AB1 4 VAL E 14 VAL E 16 0 SHEET 2 AB1 4 PHE E 76 SER E 79 -1 O PHE E 76 N VAL E 16 SHEET 3 AB1 4 PHE E 41 VAL E 48 -1 N HIS E 45 O SER E 79 SHEET 4 AB1 4 GLN E 51 SER E 59 -1 O GLY E 56 N LEU E 44 CRYST1 79.961 79.961 143.625 90.00 90.00 90.00 P 43 21 2 40 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 0.012506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012506 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006963 0.00000