HEADER CHAPERONE 08-OCT-21 7VMF TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA HDT2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE HDT2; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: HD-TUINS PROTEIN 2,HISTONE DEACETYLASE 2B; 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: HDT2, HD2, HD2B, HDA4, AT5G22650, MDJ22.7; 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 HDT, HD-TUIN, NUCLEOPLASMIN, HISTONE CHAPERONE, HD2B, HDT2, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,R.C.BOBDE,D.VASUDEVAN REVDAT 3 29-NOV-23 7VMF 1 REMARK REVDAT 2 14-DEC-22 7VMF 1 JRNL REVDAT 1 21-SEP-22 7VMF 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. 1.32 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 106115 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5549 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) : 1.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6472 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 341 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3613 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : 0.50000 REMARK 3 B33 (A**2) : 0.24000 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.786 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3695 ; 0.017 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3501 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5011 ; 1.710 ; 1.873 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8137 ; 1.053 ; 2.853 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 6.926 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;39.115 ;26.071 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 631 ;10.836 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 593 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4112 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 740 ; 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): 1901 ; 1.969 ; 1.938 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1900 ; 1.968 ; 1.937 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2368 ; 2.536 ; 2.917 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2369 ; 2.536 ; 2.919 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1794 ; 2.790 ; 2.340 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1795 ; 2.789 ; 2.341 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2643 ; 3.370 ; 3.338 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3792 ; 3.651 ;24.359 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3715 ; 3.628 ;24.086 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7196 ; 3.228 ; 3.000 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 : 1.40 REMARK 3 ION PROBE RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 1.10 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7VMF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024965. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07227 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 111734 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 49.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 6J2Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM PHOSPHATE DIBASIC PH REMARK 280 -8.0, 20%W/V PEG 3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.14950 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 98.14950 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 1.000000 0.000000 0.000000 26.55300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.11050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.55300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.11050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 98.14950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.55300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.11050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 98.14950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.55300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.11050 REMARK 290 SMTRY3 8 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 LEU B 96 REMARK 465 LEU C 96 REMARK 465 LEU D 96 REMARK 465 LEU E 96 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 C 150 O HOH C 153 1.99 REMARK 500 OE2 GLU D 76 O HOH D 201 2.06 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 GLN B 28 CA GLN B 28 CB -0.132 REMARK 500 PHE C 67 CB PHE C 67 CG -0.110 REMARK 500 PHE D 67 CB PHE D 67 CG -0.102 REMARK 500 PHE E 67 CB PHE E 67 CG -0.106 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 PHE C 67 CB - CA - C ANGL. DEV. = -14.4 DEGREES REMARK 500 MET D 1 CG - SD - CE ANGL. DEV. = 10.7 DEGREES REMARK 500 PHE D 67 CB - CA - C ANGL. DEV. = -13.4 DEGREES REMARK 500 GLU D 76 CA - CB - CG ANGL. DEV. = 13.7 DEGREES REMARK 500 PHE E 67 CB - CA - C ANGL. DEV. = -14.8 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 LYS D 11 -14.56 80.76 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 GLY D 49 ALA D 50 -147.43 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 C 169 DISTANCE = 7.44 ANGSTROMS DBREF 7VMF A 1 95 UNP Q56WH4 HDT2_ARATH 1 95 DBREF 7VMF B 1 95 UNP Q56WH4 HDT2_ARATH 1 95 DBREF 7VMF C 1 95 UNP Q56WH4 HDT2_ARATH 1 95 DBREF 7VMF D 1 95 UNP Q56WH4 HDT2_ARATH 1 95 DBREF 7VMF E 1 95 UNP Q56WH4 HDT2_ARATH 1 95 SEQADV 7VMF LEU A 96 UNP Q56WH4 EXPRESSION TAG SEQADV 7VMF LEU B 96 UNP Q56WH4 EXPRESSION TAG SEQADV 7VMF LEU C 96 UNP Q56WH4 EXPRESSION TAG SEQADV 7VMF LEU D 96 UNP Q56WH4 EXPRESSION TAG SEQADV 7VMF LEU E 96 UNP Q56WH4 EXPRESSION TAG SEQRES 1 A 96 MET GLU PHE TRP GLY VAL ALA VAL THR PRO LYS ASN ALA SEQRES 2 A 96 THR LYS VAL THR PRO GLU GLU ASP SER LEU VAL HIS ILE SEQRES 3 A 96 SER GLN ALA SER LEU ASP CYS THR VAL LYS SER GLY GLU SEQRES 4 A 96 SER VAL VAL LEU SER VAL THR VAL GLY GLY ALA LYS LEU SEQRES 5 A 96 VAL ILE GLY THR LEU SER GLN ASP LYS PHE PRO GLN ILE SEQRES 6 A 96 SER PHE ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SER SEQRES 7 A 96 HIS SER GLY THR LYS ALA ASN VAL HIS PHE ILE GLY TYR SEQRES 8 A 96 LYS SER PRO ASN LEU SEQRES 1 B 96 MET GLU PHE TRP GLY VAL ALA VAL THR PRO LYS ASN ALA SEQRES 2 B 96 THR LYS VAL THR PRO GLU GLU ASP SER LEU VAL HIS ILE SEQRES 3 B 96 SER GLN ALA SER LEU ASP CYS THR VAL LYS SER GLY GLU SEQRES 4 B 96 SER VAL VAL LEU SER VAL THR VAL GLY GLY ALA LYS LEU SEQRES 5 B 96 VAL ILE GLY THR LEU SER GLN ASP LYS PHE PRO GLN ILE SEQRES 6 B 96 SER PHE ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SER SEQRES 7 B 96 HIS SER GLY THR LYS ALA ASN VAL HIS PHE ILE GLY TYR SEQRES 8 B 96 LYS SER PRO ASN LEU SEQRES 1 C 96 MET GLU PHE TRP GLY VAL ALA VAL THR PRO LYS ASN ALA SEQRES 2 C 96 THR LYS VAL THR PRO GLU GLU ASP SER LEU VAL HIS ILE SEQRES 3 C 96 SER GLN ALA SER LEU ASP CYS THR VAL LYS SER GLY GLU SEQRES 4 C 96 SER VAL VAL LEU SER VAL THR VAL GLY GLY ALA LYS LEU SEQRES 5 C 96 VAL ILE GLY THR LEU SER GLN ASP LYS PHE PRO GLN ILE SEQRES 6 C 96 SER PHE ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SER SEQRES 7 C 96 HIS SER GLY THR LYS ALA ASN VAL HIS PHE ILE GLY TYR SEQRES 8 C 96 LYS SER PRO ASN LEU SEQRES 1 D 96 MET GLU PHE TRP GLY VAL ALA VAL THR PRO LYS ASN ALA SEQRES 2 D 96 THR LYS VAL THR PRO GLU GLU ASP SER LEU VAL HIS ILE SEQRES 3 D 96 SER GLN ALA SER LEU ASP CYS THR VAL LYS SER GLY GLU SEQRES 4 D 96 SER VAL VAL LEU SER VAL THR VAL GLY GLY ALA LYS LEU SEQRES 5 D 96 VAL ILE GLY THR LEU SER GLN ASP LYS PHE PRO GLN ILE SEQRES 6 D 96 SER PHE ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SER SEQRES 7 D 96 HIS SER GLY THR LYS ALA ASN VAL HIS PHE ILE GLY TYR SEQRES 8 D 96 LYS SER PRO ASN LEU SEQRES 1 E 96 MET GLU PHE TRP GLY VAL ALA VAL THR PRO LYS ASN ALA SEQRES 2 E 96 THR LYS VAL THR PRO GLU GLU ASP SER LEU VAL HIS ILE SEQRES 3 E 96 SER GLN ALA SER LEU ASP CYS THR VAL LYS SER GLY GLU SEQRES 4 E 96 SER VAL VAL LEU SER VAL THR VAL GLY GLY ALA LYS LEU SEQRES 5 E 96 VAL ILE GLY THR LEU SER GLN ASP LYS PHE PRO GLN ILE SEQRES 6 E 96 SER PHE ASP LEU VAL PHE ASP LYS GLU PHE GLU LEU SER SEQRES 7 E 96 HIS SER GLY THR LYS ALA ASN VAL HIS PHE ILE GLY TYR SEQRES 8 E 96 LYS SER PRO ASN LEU HET NA D 101 1 HETNAM NA SODIUM ION FORMUL 6 NA NA 1+ FORMUL 7 HOH *330(H2 O) SHEET 1 AA1 4 GLU A 2 VAL A 8 0 SHEET 2 AA1 4 ALA A 84 PRO A 94 -1 O PHE A 88 N VAL A 6 SHEET 3 AA1 4 SER A 22 CYS A 33 -1 N HIS A 25 O TYR A 91 SHEET 4 AA1 4 GLN A 64 PHE A 71 -1 O PHE A 67 N SER A 27 SHEET 1 AA2 4 THR A 14 VAL A 16 0 SHEET 2 AA2 4 PHE A 75 HIS A 79 -1 O PHE A 75 N VAL A 16 SHEET 3 AA2 4 VAL A 41 VAL A 47 -1 N SER A 44 O SER A 78 SHEET 4 AA2 4 ALA A 50 LEU A 57 -1 O GLY A 55 N LEU A 43 SHEET 1 AA3 4 GLU B 2 VAL B 8 0 SHEET 2 AA3 4 ALA B 84 PRO B 94 -1 O GLY B 90 N TRP B 4 SHEET 3 AA3 4 SER B 22 CYS B 33 -1 N HIS B 25 O TYR B 91 SHEET 4 AA3 4 GLN B 64 PHE B 71 -1 O PHE B 71 N VAL B 24 SHEET 1 AA4 4 THR B 14 VAL B 16 0 SHEET 2 AA4 4 PHE B 75 HIS B 79 -1 O PHE B 75 N VAL B 16 SHEET 3 AA4 4 VAL B 41 VAL B 47 -1 N SER B 44 O SER B 78 SHEET 4 AA4 4 ALA B 50 LEU B 57 -1 O GLY B 55 N LEU B 43 SHEET 1 AA5 4 GLU C 2 VAL C 8 0 SHEET 2 AA5 4 ALA C 84 PRO C 94 -1 O VAL C 86 N VAL C 8 SHEET 3 AA5 4 SER C 22 CYS C 33 -1 N HIS C 25 O TYR C 91 SHEET 4 AA5 4 GLN C 64 PHE C 71 -1 O PHE C 71 N VAL C 24 SHEET 1 AA6 4 THR C 14 VAL C 16 0 SHEET 2 AA6 4 PHE C 75 HIS C 79 -1 O PHE C 75 N VAL C 16 SHEET 3 AA6 4 VAL C 41 VAL C 47 -1 N SER C 44 O SER C 78 SHEET 4 AA6 4 ALA C 50 LEU C 57 -1 O GLY C 55 N LEU C 43 SHEET 1 AA7 4 GLU D 2 VAL D 8 0 SHEET 2 AA7 4 ALA D 84 PRO D 94 -1 O VAL D 86 N VAL D 8 SHEET 3 AA7 4 SER D 22 CYS D 33 -1 N HIS D 25 O TYR D 91 SHEET 4 AA7 4 GLN D 64 PHE D 71 -1 O PHE D 71 N VAL D 24 SHEET 1 AA8 4 THR D 14 VAL D 16 0 SHEET 2 AA8 4 PHE D 75 HIS D 79 -1 O PHE D 75 N VAL D 16 SHEET 3 AA8 4 VAL D 41 VAL D 47 -1 N SER D 44 O SER D 78 SHEET 4 AA8 4 ALA D 50 LEU D 57 -1 O GLY D 55 N LEU D 43 SHEET 1 AA9 4 GLU E 2 VAL E 8 0 SHEET 2 AA9 4 ALA E 84 PRO E 94 -1 O VAL E 86 N VAL E 8 SHEET 3 AA9 4 SER E 22 CYS E 33 -1 N HIS E 25 O TYR E 91 SHEET 4 AA9 4 GLN E 64 PHE E 71 -1 O PHE E 71 N VAL E 24 SHEET 1 AB1 4 THR E 14 VAL E 16 0 SHEET 2 AB1 4 PHE E 75 HIS E 79 -1 O PHE E 75 N VAL E 16 SHEET 3 AB1 4 VAL E 41 VAL E 47 -1 N SER E 44 O SER E 78 SHEET 4 AB1 4 ALA E 50 LEU E 57 -1 O GLY E 55 N LEU E 43 LINK OD1 ASN D 95 NA NA D 101 1555 1555 2.64 CRYST1 53.106 96.221 196.299 90.00 90.00 90.00 C 2 2 21 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 0.018830 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005094 0.00000