PDB Short entry for 5EEA HEADER TRANSCRIPTION 22-OCT-15 5EEA TITLE STRUCTURE OF HOXB13-DNA(CAA) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3'); COMPND 4 CHAIN: D, C, H, K; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'); COMPND 9 CHAIN: E, F, I, L; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HOMEOBOX PROTEIN HOX-B13; COMPND 13 CHAIN: B, A, G, J; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: HOXB13; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PETG20A KEYWDS TRANSCRIPTION FACTOR, DNA, COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.MORGUNOVA,Y.YIN,A.JOLMA,A.POPOV,J.TAIPALE REVDAT 4 10-JAN-24 5EEA 1 REMARK REVDAT 3 30-OCT-19 5EEA 1 REMARK LINK REVDAT 2 15-AUG-18 5EEA 1 JRNL REVDAT 1 26-OCT-16 5EEA 0 JRNL AUTH E.MORGUNOVA,Y.YIN,P.K.DAS,A.JOLMA,F.ZHU,A.POPOV,Y.XU, JRNL AUTH 2 L.NILSSON,J.TAIPALE JRNL TITL TWO DISTINCT DNA SEQUENCES RECOGNIZED BY TRANSCRIPTION JRNL TITL 2 FACTORS REPRESENT ENTHALPY AND ENTROPY OPTIMA. JRNL REF ELIFE V. 7 2018 JRNL REFN ESSN 2050-084X JRNL PMID 29638214 JRNL DOI 10.7554/ELIFE.32963 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 85430 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.9551 - 5.7489 0.97 4631 137 0.2095 0.2476 REMARK 3 2 5.7489 - 4.5644 1.00 4743 139 0.2072 0.2215 REMARK 3 3 4.5644 - 3.9878 0.99 4731 129 0.2196 0.2435 REMARK 3 4 3.9878 - 3.6234 0.99 4698 135 0.2217 0.2568 REMARK 3 5 3.6234 - 3.3637 0.97 4635 126 0.2100 0.2713 REMARK 3 6 3.3637 - 3.1655 0.96 4562 140 0.2330 0.2758 REMARK 3 7 3.1655 - 3.0070 0.98 4610 168 0.2625 0.3256 REMARK 3 8 3.0070 - 2.8761 0.98 4688 140 0.2722 0.3771 REMARK 3 9 2.8761 - 2.7654 0.99 4679 141 0.3001 0.4258 REMARK 3 10 2.7654 - 2.6700 0.98 4658 136 0.3008 0.3821 REMARK 3 11 2.6700 - 2.5865 0.98 4673 135 0.2788 0.3020 REMARK 3 12 2.5865 - 2.5126 0.99 4710 130 0.2933 0.3366 REMARK 3 13 2.5126 - 2.4464 0.97 4653 154 0.2971 0.3886 REMARK 3 14 2.4464 - 2.3867 0.98 4629 132 0.3024 0.3517 REMARK 3 15 2.3867 - 2.3325 0.98 4664 125 0.3118 0.3160 REMARK 3 16 2.3325 - 2.2829 0.97 4572 144 0.3444 0.4682 REMARK 3 17 2.2829 - 2.2372 0.99 4666 160 0.3487 0.3554 REMARK 3 18 2.2372 - 2.1950 0.78 3770 87 0.3943 0.3641 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.640 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 5451 REMARK 3 ANGLE : 1.264 7925 REMARK 3 CHIRALITY : 0.076 879 REMARK 3 PLANARITY : 0.007 496 REMARK 3 DIHEDRAL : 28.466 2320 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5EEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214775. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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) : 0.972420 REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44173 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 46.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 1.13500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5EDN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000, POTASSIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, PEG 400, PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -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 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 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: 3590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, B 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: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F, A 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: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, I, G 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: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: K, L, J 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 VAL B 278 REMARK 465 LYS B 279 REMARK 465 LYS A 279 REMARK 465 VAL J 278 REMARK 465 LYS J 279 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 G 279 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 P DG E 1 O HOH E 101 0.27 REMARK 500 N4 DC D 18 O6 DG E 1 0.36 REMARK 500 N3 DC D 18 N1 DG E 1 1.03 REMARK 500 C4 DC D 18 O6 DG E 1 1.04 REMARK 500 N2 DG I 1 O HOH I 101 1.15 REMARK 500 N4 DC D 18 C6 DG E 1 1.18 REMARK 500 OP1 DG E 1 O HOH E 101 1.25 REMARK 500 OP2 DG E 1 O HOH E 101 1.50 REMARK 500 OG SER J 224 O HOH J 301 1.64 REMARK 500 C4 DC D 18 C6 DG E 1 1.64 REMARK 500 O HOH J 324 O HOH J 332 1.71 REMARK 500 N3 DC D 18 C6 DG E 1 1.79 REMARK 500 C2 DG I 1 O HOH I 101 1.84 REMARK 500 O5' DG E 1 O HOH E 101 1.84 REMARK 500 C5' DG E 1 O HOH E 106 1.94 REMARK 500 C4 DC D 18 N1 DG E 1 1.97 REMARK 500 N4 DC H 18 O6 DG I 1 1.97 REMARK 500 N3 DC D 18 O6 DG E 1 2.07 REMARK 500 O HOH K 107 O HOH J 332 2.07 REMARK 500 N GLN J 227 O HOH J 301 2.08 REMARK 500 C5 DC D 18 O6 DG E 1 2.11 REMARK 500 OP2 DA E 11 O HOH E 102 2.13 REMARK 500 C2 DC D 18 N1 DG E 1 2.14 REMARK 500 OP2 DC H 18 O HOH H 101 2.14 REMARK 500 N1 DG I 1 O HOH I 101 2.15 REMARK 500 OP2 DA L 11 O HOH L 101 2.15 REMARK 500 OP2 DA F 11 O HOH F 101 2.15 REMARK 500 N2 DG L 1 O HOH L 102 2.16 REMARK 500 O2 DC D 18 N2 DG E 1 2.16 REMARK 500 NH1 ARG B 229 O HOH B 301 2.17 REMARK 500 OP2 DA E 12 O HOH E 103 2.18 REMARK 500 O LYS J 243 O HOH J 302 2.18 REMARK 500 N4 DC D 18 C5 DG E 1 2.19 REMARK 500 NE2 GLN J 265 O HOH J 303 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O4' DG I 1 O4' DC K 18 2545 0.71 REMARK 500 N3 DG I 1 C2' DC K 18 2545 1.66 REMARK 500 C1' DG I 1 C3' DC K 18 2545 1.72 REMARK 500 O4' DG I 1 C4' DC K 18 2545 1.73 REMARK 500 C1' DG I 1 O4' DC K 18 2545 1.79 REMARK 500 O4' DG I 1 C1' DC K 18 2545 1.89 REMARK 500 C4' DG I 1 O4' DC K 18 2545 2.01 REMARK 500 C1' DG I 1 C4' DC K 18 2545 2.05 REMARK 500 C8 DG I 1 C6 DC K 18 2545 2.06 REMARK 500 C1' DG I 1 C2' DC K 18 2545 2.15 REMARK 500 C4 DG I 1 C2' DC K 18 2545 2.17 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 D 18 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC E 16 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC F 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA F 17 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC H 18 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC I 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC K 18 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC K 18 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC K 18 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC L 16 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 ARG B 220 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 246 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 220 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 246 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG G 220 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG G 246 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG J 220 NE - CZ - NH2 ANGL. DEV. = -3.1 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 A 277 110.09 -160.11 REMARK 500 LEU G 275 -82.47 -67.64 REMARK 500 LYS G 277 86.22 -167.78 REMARK 500 LYS J 218 -70.01 -93.00 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 LEU G 275 ALA G 276 60.21 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 B 350 DISTANCE = 6.39 ANGSTROMS DBREF 5EEA D 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA E 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA C 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA F 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA H 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA I 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA K 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA L 1 18 PDB 5EEA 5EEA 1 18 DBREF 5EEA B 217 279 UNP Q92826 HXB13_HUMAN 217 279 DBREF 5EEA A 217 279 UNP Q92826 HXB13_HUMAN 217 279 DBREF 5EEA G 217 279 UNP Q92826 HXB13_HUMAN 217 279 DBREF 5EEA J 217 279 UNP Q92826 HXB13_HUMAN 217 279 SEQRES 1 D 18 DT DT DG DT DG DT DT DT DT DA DT DT DG SEQRES 2 D 18 DG DG DT DC DC SEQRES 1 E 18 DG DG DA DC DC DC DA DA DT DA DA DA DA SEQRES 2 E 18 DC DA DC DA DA SEQRES 1 C 18 DT DT DG DT DG DT DT DT DT DA DT DT DG SEQRES 2 C 18 DG DG DT DC DC SEQRES 1 F 18 DG DG DA DC DC DC DA DA DT DA DA DA DA SEQRES 2 F 18 DC DA DC DA DA SEQRES 1 H 18 DT DT DG DT DG DT DT DT DT DA DT DT DG SEQRES 2 H 18 DG DG DT DC DC SEQRES 1 I 18 DG DG DA DC DC DC DA DA DT DA DA DA DA SEQRES 2 I 18 DC DA DC DA DA SEQRES 1 K 18 DT DT DG DT DG DT DT DT DT DA DT DT DG SEQRES 2 K 18 DG DG DT DC DC SEQRES 1 L 18 DG DG DA DC DC DC DA DA DT DA DA DA DA SEQRES 2 L 18 DC DA DC DA DA SEQRES 1 B 63 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 B 63 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 B 63 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 B 63 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 B 63 VAL LYS GLU LYS LYS VAL LEU ALA LYS VAL LYS SEQRES 1 A 63 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 A 63 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 A 63 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 A 63 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 A 63 VAL LYS GLU LYS LYS VAL LEU ALA LYS VAL LYS SEQRES 1 G 63 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 G 63 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 G 63 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 G 63 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 G 63 VAL LYS GLU LYS LYS VAL LEU ALA LYS VAL LYS SEQRES 1 J 63 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 J 63 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 J 63 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 J 63 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 J 63 VAL LYS GLU LYS LYS VAL LEU ALA LYS VAL LYS FORMUL 13 HOH *518(H2 O) HELIX 1 AA1 SER B 224 ASN B 238 1 15 HELIX 2 AA2 THR B 242 SER B 254 1 13 HELIX 3 AA3 SER B 256 ALA B 276 1 21 HELIX 4 AA4 SER A 224 ASN A 238 1 15 HELIX 5 AA5 THR A 242 SER A 254 1 13 HELIX 6 AA6 SER A 256 ALA A 276 1 21 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 LEU J 275 1 20 CISPEP 1 ARG A 217 LYS A 218 0 5.41 CISPEP 2 LYS A 218 LYS A 219 0 12.53 CISPEP 3 ARG G 217 LYS G 218 0 -8.71 CISPEP 4 LYS G 218 LYS G 219 0 21.00 CISPEP 5 LYS G 277 VAL G 278 0 -20.09 CISPEP 6 ARG J 217 LYS J 218 0 9.44 CISPEP 7 LYS J 218 LYS J 219 0 10.42 CRYST1 77.356 57.918 101.278 90.00 101.57 90.00 P 1 2 1 8 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 0.012927 0.000000 0.002647 0.00000 SCALE2 0.000000 0.017266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010079 0.00000