HEADER CHAPERONE 08-OCT-21 7VMI TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA HDT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE HDT3; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: HD-TUINS PROTEIN 3,HISTONE DEACETYLASE 2C; 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: HDT3, HD2C, AT5G03740, F17C15_160, MED24.1; 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, HD2C, HDT3, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR R.C.BOBDE,A.KUMAR,D.VASUDEVAN REVDAT 3 29-NOV-23 7VMI 1 REMARK REVDAT 2 14-DEC-22 7VMI 1 JRNL REVDAT 1 21-SEP-22 7VMI 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 40545 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2164 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2986 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3801 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.63000 REMARK 3 B22 (A**2) : 7.64000 REMARK 3 B33 (A**2) : -2.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.41000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.812 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3891 ; 0.015 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3722 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5276 ; 1.759 ; 1.876 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8595 ; 1.103 ; 2.803 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 475 ; 8.091 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;32.826 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 676 ;15.729 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.523 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 600 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4330 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 850 ; 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): 1915 ; 1.672 ; 0.884 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1914 ; 1.665 ; 0.883 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2385 ; 2.783 ; 1.312 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2386 ; 2.782 ; 1.314 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1976 ; 2.054 ; 1.065 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1977 ; 2.054 ; 1.067 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2892 ; 3.168 ; 1.520 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4045 ; 6.095 ;10.912 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4018 ; 6.099 ;10.717 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): 29.4760 2.8700 5.5570 REMARK 3 T TENSOR REMARK 3 T11: 0.3505 T22: 0.4078 REMARK 3 T33: 0.3395 T12: -0.1212 REMARK 3 T13: 0.0351 T23: 0.0189 REMARK 3 L TENSOR REMARK 3 L11: 2.7524 L22: 2.0101 REMARK 3 L33: 2.8729 L12: -0.3940 REMARK 3 L13: 0.4593 L23: 0.2119 REMARK 3 S TENSOR REMARK 3 S11: -0.1414 S12: 0.8099 S13: 0.2131 REMARK 3 S21: -0.2251 S22: 0.1559 S23: -0.2084 REMARK 3 S31: -0.2671 S32: 0.4718 S33: -0.0144 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 96 REMARK 3 ORIGIN FOR THE GROUP (A): 1.6050 5.2320 21.7100 REMARK 3 T TENSOR REMARK 3 T11: 0.3449 T22: 0.0118 REMARK 3 T33: 0.3351 T12: 0.0169 REMARK 3 T13: -0.0113 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 4.0434 L22: 2.0601 REMARK 3 L33: 1.6866 L12: 0.4181 REMARK 3 L13: 0.1119 L23: 0.3103 REMARK 3 S TENSOR REMARK 3 S11: -0.0745 S12: 0.0141 S13: 0.3158 REMARK 3 S21: 0.1049 S22: -0.0333 S23: 0.1234 REMARK 3 S31: -0.1327 S32: -0.1378 S33: 0.1079 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 96 REMARK 3 ORIGIN FOR THE GROUP (A): 12.7740 -8.7030 30.4620 REMARK 3 T TENSOR REMARK 3 T11: 0.3125 T22: 0.0842 REMARK 3 T33: 0.3135 T12: -0.0021 REMARK 3 T13: 0.0160 T23: 0.0352 REMARK 3 L TENSOR REMARK 3 L11: 3.5549 L22: 2.5022 REMARK 3 L33: 2.5135 L12: 0.8376 REMARK 3 L13: 0.7122 L23: 0.2265 REMARK 3 S TENSOR REMARK 3 S11: 0.0500 S12: -0.5221 S13: -0.2947 REMARK 3 S21: 0.1554 S22: -0.0577 S23: -0.0828 REMARK 3 S31: 0.1058 S32: 0.0088 S33: 0.0077 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): 11.9350 12.4610 6.3580 REMARK 3 T TENSOR REMARK 3 T11: 0.4244 T22: 0.2115 REMARK 3 T33: 0.4264 T12: -0.0735 REMARK 3 T13: -0.0339 T23: 0.1763 REMARK 3 L TENSOR REMARK 3 L11: 3.7232 L22: 1.9383 REMARK 3 L33: 2.5658 L12: 0.0321 REMARK 3 L13: 0.4189 L23: 0.5863 REMARK 3 S TENSOR REMARK 3 S11: -0.1249 S12: 0.6809 S13: 0.6256 REMARK 3 S21: -0.1661 S22: 0.0289 S23: 0.1077 REMARK 3 S31: -0.3859 S32: 0.0068 S33: 0.0960 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 96 REMARK 3 ORIGIN FOR THE GROUP (A): 30.0950 -9.9080 20.6330 REMARK 3 T TENSOR REMARK 3 T11: 0.3158 T22: 0.1250 REMARK 3 T33: 0.3660 T12: 0.0110 REMARK 3 T13: -0.0071 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 4.5569 L22: 1.7227 REMARK 3 L33: 1.9488 L12: 0.0848 REMARK 3 L13: -0.7239 L23: 0.0384 REMARK 3 S TENSOR REMARK 3 S11: -0.0562 S12: 0.1146 S13: -0.4888 REMARK 3 S21: 0.0826 S22: 0.1123 S23: -0.2309 REMARK 3 S31: 0.1312 S32: 0.4126 S33: -0.0561 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 7VMI 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_1300024966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 7.0 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 : 46503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 45.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 43.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SUCCINIC ACID PH 7.0, 0.1 M REMARK 280 BICINE, 30% V/V PEG MME 550, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 38.80000 REMARK 290 SMTRY3 2 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: 8500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 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 D 83 CG CD CE NZ 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 C 2 CD GLU C 2 OE2 -0.070 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 ASN A 37 12.75 81.62 REMARK 500 SER A 50 -73.85 92.73 REMARK 500 ASP A 51 119.81 -30.12 REMARK 500 THR B 39 143.04 70.84 REMARK 500 ASN C 10 -161.60 57.63 REMARK 500 ASN C 36 -75.08 -148.68 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 B 35 ASN B 36 -149.62 REMARK 500 LYS C 35 ASN C 36 145.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VMI A 1 95 UNP Q9LZR5 HDT3_ARATH 1 95 DBREF 7VMI B 1 95 UNP Q9LZR5 HDT3_ARATH 1 95 DBREF 7VMI C 1 95 UNP Q9LZR5 HDT3_ARATH 1 95 DBREF 7VMI D 1 95 UNP Q9LZR5 HDT3_ARATH 1 95 DBREF 7VMI E 1 95 UNP Q9LZR5 HDT3_ARATH 1 95 SEQADV 7VMI LEU A 96 UNP Q9LZR5 EXPRESSION TAG SEQADV 7VMI LEU B 96 UNP Q9LZR5 EXPRESSION TAG SEQADV 7VMI LEU C 96 UNP Q9LZR5 EXPRESSION TAG SEQADV 7VMI LEU D 96 UNP Q9LZR5 EXPRESSION TAG SEQADV 7VMI LEU E 96 UNP Q9LZR5 EXPRESSION TAG SEQRES 1 A 96 MET GLU PHE TRP GLY VAL GLU VAL LYS ASN GLY LYS PRO SEQRES 2 A 96 LEU HIS LEU ASP PRO GLY LEU ASP ARG LEU VAL HIS ILE SEQRES 3 A 96 SER GLN VAL ALA LEU GLY GLU SER LYS ASN ASN VAL THR SEQRES 4 A 96 GLU PRO ILE GLN LEU TYR VAL THR VAL GLY SER ASP LYS SEQRES 5 A 96 LEU LEU ILE GLY THR LEU SER HIS GLU LYS PHE PRO GLN SEQRES 6 A 96 LEU SER THR GLU ILE VAL LEU GLU ARG ASN PHE ALA LEU SEQRES 7 A 96 SER HIS THR TRP LYS ASN GLY SER VAL PHE PHE SER GLY SEQRES 8 A 96 TYR LYS VAL ASP LEU SEQRES 1 B 96 MET GLU PHE TRP GLY VAL GLU VAL LYS ASN GLY LYS PRO SEQRES 2 B 96 LEU HIS LEU ASP PRO GLY LEU ASP ARG LEU VAL HIS ILE SEQRES 3 B 96 SER GLN VAL ALA LEU GLY GLU SER LYS ASN ASN VAL THR SEQRES 4 B 96 GLU PRO ILE GLN LEU TYR VAL THR VAL GLY SER ASP LYS SEQRES 5 B 96 LEU LEU ILE GLY THR LEU SER HIS GLU LYS PHE PRO GLN SEQRES 6 B 96 LEU SER THR GLU ILE VAL LEU GLU ARG ASN PHE ALA LEU SEQRES 7 B 96 SER HIS THR TRP LYS ASN GLY SER VAL PHE PHE SER GLY SEQRES 8 B 96 TYR LYS VAL ASP LEU SEQRES 1 C 96 MET GLU PHE TRP GLY VAL GLU VAL LYS ASN GLY LYS PRO SEQRES 2 C 96 LEU HIS LEU ASP PRO GLY LEU ASP ARG LEU VAL HIS ILE SEQRES 3 C 96 SER GLN VAL ALA LEU GLY GLU SER LYS ASN ASN VAL THR SEQRES 4 C 96 GLU PRO ILE GLN LEU TYR VAL THR VAL GLY SER ASP LYS SEQRES 5 C 96 LEU LEU ILE GLY THR LEU SER HIS GLU LYS PHE PRO GLN SEQRES 6 C 96 LEU SER THR GLU ILE VAL LEU GLU ARG ASN PHE ALA LEU SEQRES 7 C 96 SER HIS THR TRP LYS ASN GLY SER VAL PHE PHE SER GLY SEQRES 8 C 96 TYR LYS VAL ASP LEU SEQRES 1 D 96 MET GLU PHE TRP GLY VAL GLU VAL LYS ASN GLY LYS PRO SEQRES 2 D 96 LEU HIS LEU ASP PRO GLY LEU ASP ARG LEU VAL HIS ILE SEQRES 3 D 96 SER GLN VAL ALA LEU GLY GLU SER LYS ASN ASN VAL THR SEQRES 4 D 96 GLU PRO ILE GLN LEU TYR VAL THR VAL GLY SER ASP LYS SEQRES 5 D 96 LEU LEU ILE GLY THR LEU SER HIS GLU LYS PHE PRO GLN SEQRES 6 D 96 LEU SER THR GLU ILE VAL LEU GLU ARG ASN PHE ALA LEU SEQRES 7 D 96 SER HIS THR TRP LYS ASN GLY SER VAL PHE PHE SER GLY SEQRES 8 D 96 TYR LYS VAL ASP LEU SEQRES 1 E 96 MET GLU PHE TRP GLY VAL GLU VAL LYS ASN GLY LYS PRO SEQRES 2 E 96 LEU HIS LEU ASP PRO GLY LEU ASP ARG LEU VAL HIS ILE SEQRES 3 E 96 SER GLN VAL ALA LEU GLY GLU SER LYS ASN ASN VAL THR SEQRES 4 E 96 GLU PRO ILE GLN LEU TYR VAL THR VAL GLY SER ASP LYS SEQRES 5 E 96 LEU LEU ILE GLY THR LEU SER HIS GLU LYS PHE PRO GLN SEQRES 6 E 96 LEU SER THR GLU ILE VAL LEU GLU ARG ASN PHE ALA LEU SEQRES 7 E 96 SER HIS THR TRP LYS ASN GLY SER VAL PHE PHE SER GLY SEQRES 8 E 96 TYR LYS VAL ASP LEU FORMUL 6 HOH *116(H2 O) SHEET 1 AA1 4 GLU A 2 LYS A 9 0 SHEET 2 AA1 4 SER A 86 ASP A 95 -1 O VAL A 87 N VAL A 8 SHEET 3 AA1 4 ARG A 22 LEU A 31 -1 N ALA A 30 O PHE A 88 SHEET 4 AA1 4 GLN A 65 LEU A 72 -1 O ILE A 70 N ILE A 26 SHEET 1 AA2 4 LEU A 14 LEU A 16 0 SHEET 2 AA2 4 PHE A 76 HIS A 80 -1 O PHE A 76 N LEU A 16 SHEET 3 AA2 4 ILE A 42 VAL A 48 -1 N TYR A 45 O SER A 79 SHEET 4 AA2 4 LYS A 52 LEU A 58 -1 O LEU A 53 N VAL A 46 SHEET 1 AA3 4 GLU B 2 LYS B 9 0 SHEET 2 AA3 4 SER B 86 ASP B 95 -1 O PHE B 89 N VAL B 6 SHEET 3 AA3 4 ARG B 22 LEU B 31 -1 N ALA B 30 O PHE B 88 SHEET 4 AA3 4 GLN B 65 LEU B 72 -1 O ILE B 70 N ILE B 26 SHEET 1 AA4 4 LEU B 14 LEU B 16 0 SHEET 2 AA4 4 PHE B 76 HIS B 80 -1 O PHE B 76 N LEU B 16 SHEET 3 AA4 4 ILE B 42 VAL B 48 -1 N TYR B 45 O SER B 79 SHEET 4 AA4 4 ASP B 51 LEU B 58 -1 O LEU B 53 N VAL B 46 SHEET 1 AA5 4 GLU C 2 LYS C 9 0 SHEET 2 AA5 4 SER C 86 ASP C 95 -1 O VAL C 87 N VAL C 8 SHEET 3 AA5 4 ARG C 22 LEU C 31 -1 N ALA C 30 O PHE C 88 SHEET 4 AA5 4 GLN C 65 LEU C 72 -1 O ILE C 70 N ILE C 26 SHEET 1 AA6 4 LEU C 14 LEU C 16 0 SHEET 2 AA6 4 PHE C 76 HIS C 80 -1 O PHE C 76 N LEU C 16 SHEET 3 AA6 4 ILE C 42 VAL C 48 -1 N TYR C 45 O SER C 79 SHEET 4 AA6 4 ASP C 51 LEU C 58 -1 O LEU C 53 N VAL C 46 SHEET 1 AA7 4 GLU D 2 LYS D 9 0 SHEET 2 AA7 4 SER D 86 ASP D 95 -1 O VAL D 87 N VAL D 8 SHEET 3 AA7 4 ARG D 22 LEU D 31 -1 N ALA D 30 O PHE D 88 SHEET 4 AA7 4 GLN D 65 LEU D 72 -1 O ILE D 70 N ILE D 26 SHEET 1 AA8 4 LEU D 14 LEU D 16 0 SHEET 2 AA8 4 PHE D 76 HIS D 80 -1 O PHE D 76 N LEU D 16 SHEET 3 AA8 4 ILE D 42 VAL D 48 -1 N TYR D 45 O SER D 79 SHEET 4 AA8 4 ASP D 51 LEU D 58 -1 O LEU D 53 N VAL D 46 SHEET 1 AA9 4 GLU E 2 LYS E 9 0 SHEET 2 AA9 4 SER E 86 ASP E 95 -1 O GLY E 91 N TRP E 4 SHEET 3 AA9 4 ARG E 22 LEU E 31 -1 N ALA E 30 O PHE E 88 SHEET 4 AA9 4 GLN E 65 LEU E 72 -1 O ILE E 70 N ILE E 26 SHEET 1 AB1 4 LEU E 14 LEU E 16 0 SHEET 2 AB1 4 PHE E 76 HIS E 80 -1 O PHE E 76 N LEU E 16 SHEET 3 AB1 4 ILE E 42 VAL E 48 -1 N TYR E 45 O SER E 79 SHEET 4 AB1 4 ASP E 51 LEU E 58 -1 O LEU E 53 N VAL E 46 CRYST1 54.623 77.600 55.511 90.00 91.82 90.00 P 1 21 1 10 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 0.018307 0.000000 0.000583 0.00000 SCALE2 0.000000 0.012887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018024 0.00000