PDB Short entry for 3NM9 HEADER GENE REGULATION/DNA 22-JUN-10 3NM9 TITLE HMGD(M13A)-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH MOBILITY GROUP PROTEIN D; COMPND 3 CHAIN: A, D, G, J, M, P; COMPND 4 SYNONYM: HMG-D; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'; COMPND 9 CHAIN: B, C, E, F, H, I, K, L, N, O; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CG17950, HMGD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET13A; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-D74-M13A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS HIGH MOBILITY GROUP, DNA BENDING, NON-SEQUENCE-SPECIFIC, HMG DOMAIN, KEYWDS 2 CHROMOSOMAL PROTEIN, DNA, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.E.A.CHURCHILL,J.KLASS,D.L.ZOETEWEY REVDAT 3 06-SEP-23 3NM9 1 SEQADV REVDAT 2 08-DEC-10 3NM9 1 JRNL REVDAT 1 22-SEP-10 3NM9 0 JRNL AUTH M.E.CHURCHILL,J.KLASS,D.L.ZOETEWEY JRNL TITL STRUCTURAL ANALYSIS OF HMGD-DNA COMPLEXES REVEALS INFLUENCE JRNL TITL 2 OF INTERCALATION ON SEQUENCE SELECTIVITY AND DNA BENDING. JRNL REF J.MOL.BIOL. V. 403 88 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20800069 JRNL DOI 10.1016/J.JMB.2010.08.031 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 21700 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) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1179 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1429 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.4220 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.4490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3510 REMARK 3 NUCLEIC ACID ATOMS : 2042 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.41000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : 3.22000 REMARK 3 B12 (A**2) : -0.60000 REMARK 3 B13 (A**2) : -1.28000 REMARK 3 B23 (A**2) : -4.37000 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): 0.444 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.251 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.834 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.907 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.855 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5861 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8297 ; 1.334 ; 2.402 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 432 ; 4.973 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;35.763 ;23.571 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 696 ;23.877 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;21.277 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 868 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3748 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2129 ; 0.209 ; 0.250 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3569 ; 0.298 ; 0.250 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 230 ; 0.186 ; 0.250 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): 80 ; 0.167 ; 0.250 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.346 ; 0.250 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): 2241 ; 1.681 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3450 ; 2.821 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4847 ; 3.078 ; 3.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4847 ; 4.279 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : BLUE OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23992 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 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: 1QRV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 MM HMGDM13A PROTEIN, 1.18 MM REMARK 280 DUPLEX DNA FRAGMENT (GCGATATCGC), 5 MM MES-NA PH 5.25, 10 MM REMARK 280 NACL, AND 7.6% PEG 3350 EQUILIBRATED AGAINST 0.5 ML 32% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: HEXADECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, G, J, M, P, B, C, E, F, REMARK 350 AND CHAINS: H, I, K, L, N, O 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 DG B 1 REMARK 465 DG C 1 REMARK 465 DG E 1 REMARK 465 DG F 1 REMARK 465 DG H 1 REMARK 465 DG I 1 REMARK 465 DG K 1 REMARK 465 DG N 1 REMARK 465 DG O 1 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 DG B 2 P OP1 OP2 REMARK 470 DG C 2 P OP1 OP2 REMARK 470 DG E 2 P OP1 OP2 REMARK 470 DG F 2 P OP1 OP2 REMARK 470 DG H 2 P OP1 OP2 REMARK 470 DG I 2 P OP1 OP2 REMARK 470 DG K 2 P OP1 OP2 REMARK 470 DG N 2 P OP1 OP2 REMARK 470 DG O 2 P OP1 OP2 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 NH2 ARG D 25 OP1 DG O 10 2.17 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 DT B 6 C5 DT B 6 C7 0.126 REMARK 500 DT B 8 C5 DT B 8 C7 0.039 REMARK 500 DT C 8 C5 DT C 8 C7 0.107 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 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 6 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT C 8 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT E 8 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC E 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC E 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG F 2 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG F 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG H 4 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DG H 4 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA H 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC H 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG I 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC I 3 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA I 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT I 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT I 8 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DT I 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG K 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC K 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG K 4 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG K 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA K 5 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT K 6 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DA K 7 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC K 11 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC K 11 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG L 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC L 3 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG L 4 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG L 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC L 11 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC L 11 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC N 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG N 10 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT O 6 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DC O 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG O 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC O 11 O4' - C1' - N1 ANGL. DEV. = 7.3 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 ASP A 3 125.65 -35.32 REMARK 500 ALA A 72 -70.02 -79.40 REMARK 500 ASP D 61 -70.13 -64.71 REMARK 500 ASP D 62 -57.12 -28.14 REMARK 500 ALA G 72 -47.37 -174.45 REMARK 500 ASN G 73 37.49 -97.64 REMARK 500 ASP J 3 -127.23 -74.31 REMARK 500 ALA J 19 -10.15 -146.09 REMARK 500 VAL J 32 -37.30 -37.04 REMARK 500 GLU J 41 -17.54 -47.80 REMARK 500 ARG J 44 39.80 -56.08 REMARK 500 ALA J 45 -12.81 -167.01 REMARK 500 LYS J 47 -82.37 -90.85 REMARK 500 ASN J 73 -131.98 -90.08 REMARK 500 ALA M 19 -1.91 -140.51 REMARK 500 VAL M 32 4.36 -67.02 REMARK 500 LYS M 47 -54.68 -138.36 REMARK 500 ASN M 73 47.06 -80.86 REMARK 500 LYS P 4 115.93 -32.62 REMARK 500 SER P 50 -75.35 -68.63 REMARK 500 ALA P 72 -81.78 -75.27 REMARK 500 ASN P 73 -116.79 -79.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QRV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA DBREF 3NM9 A 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 3NM9 D 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 3NM9 G 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 3NM9 J 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 3NM9 M 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 3NM9 P 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 3NM9 B 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 C 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 E 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 F 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 H 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 I 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 K 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 L 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 N 1 11 PDB 3NM9 3NM9 1 11 DBREF 3NM9 O 1 11 PDB 3NM9 3NM9 1 11 SEQADV 3NM9 ALA A 13 UNP Q05783 MET 13 ENGINEERED MUTATION SEQADV 3NM9 ALA D 13 UNP Q05783 MET 13 ENGINEERED MUTATION SEQADV 3NM9 ALA G 13 UNP Q05783 MET 13 ENGINEERED MUTATION SEQADV 3NM9 ALA J 13 UNP Q05783 MET 13 ENGINEERED MUTATION SEQADV 3NM9 ALA M 13 UNP Q05783 MET 13 ENGINEERED MUTATION SEQADV 3NM9 ALA P 13 UNP Q05783 MET 13 ENGINEERED MUTATION SEQRES 1 A 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR ALA LEU SEQRES 2 A 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 A 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 A 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 A 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 A 73 VAL LYS GLU PHE GLU ALA ASN GLY SEQRES 1 D 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR ALA LEU SEQRES 2 D 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 D 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 D 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 D 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 D 73 VAL LYS GLU PHE GLU ALA ASN GLY SEQRES 1 G 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR ALA LEU SEQRES 2 G 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 G 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 G 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 G 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 G 73 VAL LYS GLU PHE GLU ALA ASN GLY SEQRES 1 J 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR ALA LEU SEQRES 2 J 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 J 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 J 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 J 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 J 73 VAL LYS GLU PHE GLU ALA ASN GLY SEQRES 1 M 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR ALA LEU SEQRES 2 M 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 M 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 M 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 M 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 M 73 VAL LYS GLU PHE GLU ALA ASN GLY SEQRES 1 P 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR ALA LEU SEQRES 2 P 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 P 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 P 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 P 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 P 73 VAL LYS GLU PHE GLU ALA ASN GLY SEQRES 1 B 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 C 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 E 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 F 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 H 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 I 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 K 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 L 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 N 11 DG DG DC DG DA DT DA DT DC DG DC SEQRES 1 O 11 DG DG DC DG DA DT DA DT DC DG DC FORMUL 17 HOH *4(H2 O) HELIX 1 1 SER A 10 ASN A 27 1 18 HELIX 2 2 LYS A 31 MET A 46 1 16 HELIX 3 3 LYS A 49 ASN A 73 1 25 HELIX 4 4 SER D 10 ASN D 27 1 18 HELIX 5 5 LYS D 31 MET D 46 1 16 HELIX 6 6 LYS D 49 ASN D 73 1 25 HELIX 7 7 SER G 10 SER G 18 1 9 HELIX 8 8 ALA G 19 ASN G 27 1 9 HELIX 9 9 LYS G 31 ALA G 45 1 15 HELIX 10 10 LYS G 49 GLU G 71 1 23 HELIX 11 11 SER J 10 ASN J 17 1 8 HELIX 12 12 ALA J 19 ASN J 27 1 9 HELIX 13 13 LYS J 31 ARG J 44 1 14 HELIX 14 14 LYS J 49 GLU J 71 1 23 HELIX 15 15 SER M 10 ASN M 17 1 8 HELIX 16 16 ALA M 19 ASN M 27 1 9 HELIX 17 17 THR M 33 MET M 46 1 14 HELIX 18 18 LYS M 49 ASN M 73 1 25 HELIX 19 19 SER P 10 GLU P 26 1 17 HELIX 20 20 LYS P 31 ALA P 45 1 15 HELIX 21 21 LYS P 49 ASN P 73 1 25 CRYST1 44.750 71.700 89.020 92.49 91.12 107.10 P 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 0.022346 0.006875 0.000792 0.00000 SCALE2 0.000000 0.014592 0.000752 0.00000 SCALE3 0.000000 0.000000 0.011250 0.00000