HEADER DNA BINDING PROTEIN 24-SEP-21 7PSX TITLE STRUCTURE OF HOXB13 BOUND TO HYDROXYMETHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN HOX-B13; COMPND 3 CHAIN: A, B, G, J; COMPND 4 FRAGMENT: UNP RESIDUES 217-277; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3'); COMPND 9 CHAIN: C, D, H, K; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'); COMPND 14 CHAIN: F, E, I, L; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HOXB13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETG20A-SBP; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION, HYDROXYMETHYLATION, PROTEIN-DNA COMPLEX, TRANSCRIPTION KEYWDS 2 FACTOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.MORGUNOVA,A.POPOV,Y.YIN,J.TAIPALE REVDAT 2 31-JAN-24 7PSX 1 REMARK REVDAT 1 05-OCT-22 7PSX 0 JRNL AUTH E.MORGUNOVA,A.POPOV,Y.YIN,J.TAIPALE JRNL TITL STRUCTURE OF HOXB13 BOUND TO HYDROXYMETHYLATED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 52887 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) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1603 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3881 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.4090 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2039 REMARK 3 NUCLEIC ACID ATOMS : 2968 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 356 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.88000 REMARK 3 B22 (A**2) : -1.05000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : -0.63000 REMARK 3 B13 (A**2) : 2.26000 REMARK 3 B23 (A**2) : -0.69000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.184 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.264 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.008 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5422 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3826 ; 0.002 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7895 ; 1.484 ; 1.385 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8948 ; 1.448 ; 2.207 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 247 ; 5.191 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;30.706 ;18.201 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 489 ;19.011 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;19.023 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 701 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4005 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1191 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 18 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 218 276 B 218 276 1962 0.070 0.050 REMARK 3 2 A 217 275 G 217 275 1958 0.080 0.050 REMARK 3 3 A 218 274 J 218 274 1921 0.070 0.050 REMARK 3 4 C 1 18 D 1 18 1522 0.080 0.050 REMARK 3 5 C 1 18 H 1 18 1536 0.060 0.050 REMARK 3 6 C 1 18 K 1 18 1532 0.060 0.050 REMARK 3 7 F 1 18 E 1 18 1561 0.020 0.050 REMARK 3 8 F 1 18 I 1 18 1566 0.030 0.050 REMARK 3 9 F 1 18 L 1 18 1558 0.030 0.050 REMARK 3 10 B 218 275 G 218 275 2016 0.070 0.050 REMARK 3 11 B 218 274 J 218 274 1998 0.060 0.050 REMARK 3 12 D 1 18 H 1 18 1587 0.050 0.050 REMARK 3 13 D 1 18 K 1 18 1573 0.050 0.050 REMARK 3 14 E 1 18 I 1 18 1562 0.030 0.050 REMARK 3 15 E 1 18 L 1 18 1556 0.030 0.050 REMARK 3 16 G 218 274 J 218 274 2012 0.070 0.050 REMARK 3 17 H 1 18 K 1 18 1584 0.020 0.050 REMARK 3 18 I 1 18 L 1 18 1564 0.050 0.050 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7PSX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118170. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97242 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55783 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 48.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.28400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 5.77600 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 2.8.2 REMARK 200 STARTING MODEL: 5EDN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 1000, 8% PEG 200, 0.15M KCL, REMARK 280 0.1M MGCL2, 0.05M BIS-TRIS, PH 6.8, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K 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, 2, 3, 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, F 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, I 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: J, K, L 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 ARG B 217 REMARK 465 LYS G 277 REMARK 465 ARG J 217 REMARK 465 ALA J 276 REMARK 465 LYS J 277 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 5HC F 7 P OP1 OP2 O5' C5' REMARK 480 5HC E 7 P OP1 OP2 O5' C5' REMARK 480 5HC I 7 P OP1 OP2 O5' C5' REMARK 480 5HC L 7 P OP1 OP2 O5' C5' 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 OP2 DC E 5 O HOH E 101 1.80 REMARK 500 N2 DG H 5 C2 DA I 15 2.01 REMARK 500 N2 DG H 3 N7 DA I 17 2.03 REMARK 500 OP1 DC E 5 O HOH E 102 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 DT C 1 P DT C 1 OP3 -0.122 REMARK 500 DG F 1 P DG F 1 OP3 -0.123 REMARK 500 DT D 1 P DT D 1 OP3 -0.122 REMARK 500 DG E 1 P DG E 1 OP3 -0.121 REMARK 500 DT H 1 P DT H 1 OP3 -0.122 REMARK 500 DG I 1 P DG I 1 OP3 -0.121 REMARK 500 DT K 1 P DT K 1 OP3 -0.122 REMARK 500 DG L 1 P DG L 1 OP3 -0.122 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 LEU A 275 43.56 -82.07 REMARK 500 LYS G 218 115.01 -161.54 REMARK 500 LEU G 275 48.47 -82.80 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 E 128 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH G 330 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH G 331 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH G 332 DISTANCE = 7.60 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 217 O REMARK 620 2 HOH F 121 O 89.3 REMARK 620 3 HOH F 124 O 96.3 93.8 REMARK 620 4 HOH B 438 O 170.2 84.4 91.5 REMARK 620 5 HOH B 443 O 101.3 168.9 88.4 84.7 REMARK 620 6 HOH B 452 O 89.0 91.8 172.3 83.7 85.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH E 126 O REMARK 620 2 HOH E 127 O 52.7 REMARK 620 3 HOH E 128 O 107.9 159.5 REMARK 620 N 1 2 DBREF 7PSX A 217 277 UNP Q92826 HXB13_HUMAN 217 277 DBREF 7PSX C 1 18 PDB 7PSX 7PSX 1 18 DBREF 7PSX F 1 18 PDB 7PSX 7PSX 1 18 DBREF 7PSX B 217 277 UNP Q92826 HXB13_HUMAN 217 277 DBREF 7PSX D 1 18 PDB 7PSX 7PSX 1 18 DBREF 7PSX E 1 18 PDB 7PSX 7PSX 1 18 DBREF 7PSX G 217 277 UNP Q92826 HXB13_HUMAN 217 277 DBREF 7PSX H 1 18 PDB 7PSX 7PSX 1 18 DBREF 7PSX I 1 18 PDB 7PSX 7PSX 1 18 DBREF 7PSX J 217 277 UNP Q92826 HXB13_HUMAN 217 277 DBREF 7PSX K 1 18 PDB 7PSX 7PSX 1 18 DBREF 7PSX L 1 18 PDB 7PSX 7PSX 1 18 SEQRES 1 A 61 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 A 61 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 A 61 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 A 61 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 A 61 VAL LYS GLU LYS LYS VAL LEU ALA LYS SEQRES 1 C 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 C 18 DG DG DT DC DC SEQRES 1 F 18 DG DG DA DC DC DT 5HC DA DT DA DA DA DA SEQRES 2 F 18 DC DA DC DA DA SEQRES 1 B 61 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 B 61 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 B 61 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 B 61 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 B 61 VAL LYS GLU LYS LYS VAL LEU ALA LYS SEQRES 1 D 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 D 18 DG DG DT DC DC SEQRES 1 E 18 DG DG DA DC DC DT 5HC DA DT DA DA DA DA SEQRES 2 E 18 DC DA DC DA DA SEQRES 1 G 61 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 G 61 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 G 61 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 G 61 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 G 61 VAL LYS GLU LYS LYS VAL LEU ALA LYS SEQRES 1 H 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 H 18 DG DG DT DC DC SEQRES 1 I 18 DG DG DA DC DC DT 5HC DA DT DA DA DA DA SEQRES 2 I 18 DC DA DC DA DA SEQRES 1 J 61 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 J 61 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 J 61 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 J 61 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 J 61 VAL LYS GLU LYS LYS VAL LEU ALA LYS SEQRES 1 K 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 K 18 DG DG DT DC DC SEQRES 1 L 18 DG DG DA DC DC DT 5HC DA DT DA DA DA DA SEQRES 2 L 18 DC DA DC DA DA HET 5HC F 7 21 HET 5HC E 7 21 HET 5HC I 7 21 HET 5HC L 7 21 HET MG C 101 1 HET MG B 301 1 HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) HETNAM MG MAGNESIUM ION FORMUL 3 5HC 4(C10 H16 N3 O8 P) FORMUL 13 MG 2(MG 2+) FORMUL 15 HOH *356(H2 O) HELIX 1 AA1 SER A 224 ASN A 238 1 15 HELIX 2 AA2 THR A 242 SER A 254 1 13 HELIX 3 AA3 SER A 256 LEU A 275 1 20 HELIX 4 AA4 SER B 224 ASN B 238 1 15 HELIX 5 AA5 THR B 242 SER B 254 1 13 HELIX 6 AA6 SER B 256 LYS B 277 1 22 HELIX 7 AA7 SER G 224 ASN G 238 1 15 HELIX 8 AA8 THR G 242 SER G 254 1 13 HELIX 9 AA9 SER G 256 LEU G 275 1 20 HELIX 10 AB1 SER J 224 ASN J 238 1 15 HELIX 11 AB2 THR J 242 SER J 254 1 13 HELIX 12 AB3 SER J 256 LYS J 273 1 18 LINK O3' DT F 6 P 5HC F 7 1555 1555 1.60 LINK O3' 5HC F 7 P DA F 8 1555 1555 1.60 LINK O3' DT E 6 P 5HC E 7 1555 1555 1.60 LINK O3' 5HC E 7 P DA E 8 1555 1555 1.60 LINK O3' DT I 6 P 5HC I 7 1555 1555 1.60 LINK O3' 5HC I 7 P DA I 8 1555 1555 1.60 LINK O3' DT L 6 P 5HC L 7 1555 1555 1.60 LINK O3' 5HC L 7 P DA L 8 1555 1555 1.60 LINK MG MG C 101 O HOH C 217 1555 1555 2.15 LINK MG MG C 101 O HOH F 121 1555 1555 1.80 LINK MG MG C 101 O HOH F 124 1555 1555 2.05 LINK MG MG C 101 O HOH B 438 1555 1545 2.46 LINK MG MG C 101 O HOH B 443 1555 1545 2.32 LINK MG MG C 101 O HOH B 452 1555 1545 2.19 LINK MG MG B 301 O HOH E 126 1555 1555 2.04 LINK MG MG B 301 O HOH E 127 1555 1555 2.74 LINK MG MG B 301 O HOH E 128 1555 1555 1.98 CRYST1 38.153 55.541 101.080 88.02 81.46 84.94 P 1 4 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 0.026210 -0.002322 -0.003888 0.00000 SCALE2 0.000000 0.018075 -0.000394 0.00000 SCALE3 0.000000 0.000000 0.010007 0.00000