HEADER DNA BINDING PROTEIN/DNA 21-MAY-22 7XV6 TITLE CRYSTAL STRUCTURE OF THE HUMAN TR4 DNA-BINDING DOMAIN WITH C-TERMINAL TITLE 2 EXTENSION (DBD-CTE) HOMODIMER BOUND TO DR1 RESPONSE ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*GP*CP*AP*GP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3'); COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*CP*TP*GP*C)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: NR2C2 PROTEIN; COMPND 13 CHAIN: A, B; COMPND 14 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP C MEMBER 2; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DNA MOLECULE; SOURCE 4 ORGANISM_TAXID: 2853804; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: DNA MOLECULE; SOURCE 8 ORGANISM_TAXID: 2853804; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: NR2C2; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS TRANSCRIPTIONAL REGULATION, DNA BINDING, PROTEIN-DNA COMPLEX, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,Z.CHEN REVDAT 4 29-NOV-23 7XV6 1 REMARK REVDAT 3 08-MAR-23 7XV6 1 JRNL REVDAT 2 01-FEB-23 7XV6 1 JRNL REVDAT 1 28-DEC-22 7XV6 0 JRNL AUTH Y.LIU,L.MA,M.LI,Z.TIAN,M.YANG,X.WU,X.WANG,G.SHANG,M.XIE, JRNL AUTH 2 Y.CHEN,X.LIU,L.JIANG,W.WU,C.XU,L.XIA,G.LI,S.DAI,Z.CHEN JRNL TITL STRUCTURES OF HUMAN TR4LBD-JAZF1 AND TR4DBD-DNA COMPLEXES JRNL TITL 2 REVEAL THE MOLECULAR BASIS OF TRANSCRIPTIONAL REGULATION. JRNL REF NUCLEIC ACIDS RES. V. 51 1443 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36651297 JRNL DOI 10.1093/NAR/GKAC1259 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 3 NUMBER OF REFLECTIONS : 13569 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.034 REMARK 3 FREE R VALUE TEST SET COUNT : 683 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 516 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 48.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1226 REMARK 3 NUCLEIC ACID ATOMS : 732 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03700 REMARK 3 B22 (A**2) : -0.03700 REMARK 3 B33 (A**2) : 0.07400 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): 0.346 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.220 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.465 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2061 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1544 ; 0.002 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2911 ; 1.904 ; 1.441 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3576 ; 1.523 ; 1.969 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 159 ; 7.711 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;29.265 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 231 ;15.901 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.773 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 262 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1862 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 498 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 376 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 38 ; 0.295 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 893 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 151 ; 0.175 ; 0.200 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): 641 ; 3.360 ; 3.242 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 640 ; 3.351 ; 3.238 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 798 ; 5.080 ; 4.835 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 799 ; 5.081 ; 4.842 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1420 ; 3.761 ; 3.407 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1420 ; 3.761 ; 3.407 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2113 ; 5.626 ; 5.045 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2114 ; 5.625 ; 5.048 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7XV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15386 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.297 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: BALBES REMARK 200 STARTING MODEL: 3DZU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, TRIS, AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 121.35050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.07300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.07300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 182.02575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.07300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.07300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.67525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.07300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.07300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 182.02575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.07300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.07300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.67525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 121.35050 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, 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 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 GLU B 190 REMARK 465 ARG B 191 REMARK 465 LYS B 192 REMARK 465 PRO B 193 REMARK 465 PHE B 194 REMARK 465 ASP B 195 REMARK 465 VAL B 196 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 VAL A 113 CG1 CG2 REMARK 470 GLU A 115 CD OE1 OE2 REMARK 470 LYS A 123 CG CD CE NZ REMARK 470 ARG A 127 NH1 NH2 REMARK 470 SER A 152 OG REMARK 470 ARG A 154 CZ NH1 NH2 REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 HIS A 164 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 165 CD2 CE1 NE2 REMARK 470 LYS A 183 CE NZ REMARK 470 PHE A 194 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 195 CG OD1 OD2 REMARK 470 VAL A 196 CG1 CG2 REMARK 470 VAL B 113 N CB CG1 CG2 REMARK 470 LYS B 123 CG CD CE NZ REMARK 470 LYS B 175 CE NZ REMARK 470 LYS B 176 CE NZ REMARK 470 LYS B 183 CE NZ 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 DG C 2 O5' - P - OP2 ANGL. DEV. = -8.4 DEGREES REMARK 500 DA C 6 O5' - P - OP1 ANGL. DEV. = 10.6 DEGREES REMARK 500 DA C 6 O5' - P - OP2 ANGL. DEV. = -7.6 DEGREES REMARK 500 DA C 6 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DA C 13 O5' - P - OP1 ANGL. DEV. = 11.8 DEGREES REMARK 500 DA C 13 O5' - P - OP2 ANGL. DEV. = -11.5 DEGREES REMARK 500 ARG A 143 CG - CD - NE ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG A 143 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 143 NE - CZ - NH2 ANGL. DEV. = 4.0 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 SER A 155 72.36 -166.43 REMARK 500 ASN A 156 -4.65 80.76 REMARK 500 ASP A 158 43.70 -151.90 REMARK 500 ASP A 195 70.26 60.81 REMARK 500 VAL B 119 -61.24 -90.68 REMARK 500 SER B 155 77.67 -163.71 REMARK 500 ASN B 156 15.06 59.19 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 A 149 THR A 150 149.42 REMARK 500 LEU B 149 THR B 150 148.30 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 156 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH C 157 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH C 158 DISTANCE = 8.06 ANGSTROMS REMARK 525 HOH C 159 DISTANCE = 10.04 ANGSTROMS REMARK 525 HOH A 372 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 373 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A 374 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 375 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 376 DISTANCE = 8.60 ANGSTROMS REMARK 525 HOH B 374 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B 375 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B 376 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH B 377 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH B 378 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH B 379 DISTANCE = 8.00 ANGSTROMS REMARK 525 HOH B 380 DISTANCE = 8.32 ANGSTROMS REMARK 525 HOH B 381 DISTANCE = 8.68 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 117 SG REMARK 620 2 CYS A 120 SG 111.6 REMARK 620 3 CYS A 134 SG 120.2 104.7 REMARK 620 4 CYS A 137 SG 102.0 113.8 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 153 SG REMARK 620 2 CYS A 159 SG 104.2 REMARK 620 3 CYS A 169 SG 104.2 116.7 REMARK 620 4 CYS A 172 SG 113.5 113.5 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 117 SG REMARK 620 2 CYS B 120 SG 112.5 REMARK 620 3 CYS B 134 SG 118.4 100.2 REMARK 620 4 CYS B 137 SG 107.5 114.9 103.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 153 SG REMARK 620 2 CYS B 159 SG 102.5 REMARK 620 3 CYS B 169 SG 104.5 117.5 REMARK 620 4 CYS B 172 SG 112.5 110.3 109.3 REMARK 620 N 1 2 3 DBREF 7XV6 C 1 18 PDB 7XV6 7XV6 1 18 DBREF 7XV6 D 1 18 PDB 7XV6 7XV6 1 18 DBREF1 7XV6 A 113 196 UNP A0A7L2NB91_9PASS DBREF2 7XV6 A A0A7L2NB91 113 196 DBREF1 7XV6 B 113 196 UNP A0A7L2NB91_9PASS DBREF2 7XV6 B A0A7L2NB91 113 196 SEQRES 1 C 18 DG DG DC DA DG DA DG DG DT DC DA DA DA SEQRES 2 C 18 DG DG DT DC DA SEQRES 1 D 18 DC DT DG DA DC DC DT DT DT DG DA DC DC SEQRES 2 D 18 DT DC DT DG DC SEQRES 1 A 84 VAL VAL GLU TYR CYS VAL VAL CYS GLY ASP LYS ALA SER SEQRES 2 A 84 GLY ARG HIS TYR GLY ALA VAL SER CYS GLU GLY CYS LYS SEQRES 3 A 84 GLY PHE PHE LYS ARG SER VAL ARG LYS ASN LEU THR TYR SEQRES 4 A 84 SER CYS ARG SER ASN GLN ASP CYS ILE ILE ASN LYS HIS SEQRES 5 A 84 HIS ARG ASN ARG CYS GLN PHE CYS ARG LEU LYS LYS CYS SEQRES 6 A 84 LEU GLU MET GLY MET LYS MET GLU SER VAL GLN SER GLU SEQRES 7 A 84 ARG LYS PRO PHE ASP VAL SEQRES 1 B 84 VAL VAL GLU TYR CYS VAL VAL CYS GLY ASP LYS ALA SER SEQRES 2 B 84 GLY ARG HIS TYR GLY ALA VAL SER CYS GLU GLY CYS LYS SEQRES 3 B 84 GLY PHE PHE LYS ARG SER VAL ARG LYS ASN LEU THR TYR SEQRES 4 B 84 SER CYS ARG SER ASN GLN ASP CYS ILE ILE ASN LYS HIS SEQRES 5 B 84 HIS ARG ASN ARG CYS GLN PHE CYS ARG LEU LYS LYS CYS SEQRES 6 B 84 LEU GLU MET GLY MET LYS MET GLU SER VAL GLN SER GLU SEQRES 7 B 84 ARG LYS PRO PHE ASP VAL HET ZN A 201 1 HET ZN A 202 1 HET ZN B 201 1 HET ZN B 202 1 HETNAM ZN ZINC ION FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *264(H2 O) HELIX 1 AA1 CYS A 134 LYS A 147 1 14 HELIX 2 AA2 CYS A 169 MET A 180 1 12 HELIX 3 AA3 LYS A 183 VAL A 187 5 5 HELIX 4 AA4 CYS B 134 LYS B 147 1 14 HELIX 5 AA5 CYS B 169 MET B 180 1 12 HELIX 6 AA6 LYS B 183 VAL B 187 5 5 SHEET 1 AA1 2 GLY A 126 HIS A 128 0 SHEET 2 AA1 2 ALA A 131 SER A 133 -1 O ALA A 131 N HIS A 128 SHEET 1 AA2 2 GLY B 126 HIS B 128 0 SHEET 2 AA2 2 ALA B 131 SER B 133 -1 O SER B 133 N GLY B 126 LINK SG CYS A 117 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 120 ZN ZN A 201 1555 1555 2.20 LINK SG CYS A 134 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 137 ZN ZN A 201 1555 1555 2.19 LINK SG CYS A 153 ZN ZN A 202 1555 1555 2.30 LINK SG CYS A 159 ZN ZN A 202 1555 1555 2.25 LINK SG CYS A 169 ZN ZN A 202 1555 1555 2.45 LINK SG CYS A 172 ZN ZN A 202 1555 1555 2.39 LINK SG CYS B 117 ZN ZN B 201 1555 1555 2.30 LINK SG CYS B 120 ZN ZN B 201 1555 1555 2.32 LINK SG CYS B 134 ZN ZN B 201 1555 1555 2.35 LINK SG CYS B 137 ZN ZN B 201 1555 1555 2.33 LINK SG CYS B 153 ZN ZN B 202 1555 1555 2.43 LINK SG CYS B 159 ZN ZN B 202 1555 1555 2.40 LINK SG CYS B 169 ZN ZN B 202 1555 1555 2.25 LINK SG CYS B 172 ZN ZN B 202 1555 1555 2.12 CRYST1 52.146 52.146 242.701 90.00 90.00 90.00 P 43 21 2 16 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 0.019177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004120 0.00000