HEADER TRANSCRIPTION 27-JUL-19 6SDG TITLE CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF M. POLYMORPHA AUXIN TITLE 2 RESPONSE FACTOR 2 (MPARF2) IN COMPLEX WITH HIGH AFFINITY DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUXIN RESPONSE FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 21-7_A; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 21-7_B; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARCHANTIA POLYMORPHA; SOURCE 3 ORGANISM_COMMON: LIVERWORT; SOURCE 4 ORGANISM_TAXID: 3197; SOURCE 5 GENE: MPARF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTWIN1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 14 ORGANISM_TAXID: 3702; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 18 ORGANISM_TAXID: 3702 KEYWDS TRANSCRIPTION FACTOR, DNA BINDING, NUCLEUS, HORMONE RESPONSE, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR I.CRESPO,D.WEIJERS,D.R.BOER REVDAT 3 24-JAN-24 6SDG 1 REMARK REVDAT 2 03-JUN-20 6SDG 1 JRNL REVDAT 1 08-APR-20 6SDG 0 JRNL AUTH H.KATO,S.K.MUTTE,H.SUZUKI,I.CRESPO,S.DAS,T.RADOEVA, JRNL AUTH 2 M.FONTANA,Y.YOSHITAKE,E.HAINIWA,W.VAN DEN BERG,S.LINDHOUD, JRNL AUTH 3 K.ISHIZAKI,J.HOHLBEIN,J.W.BORST,D.R.BOER,R.NISHIHAMA, JRNL AUTH 4 T.KOHCHI,D.WEIJERS JRNL TITL DESIGN PRINCIPLES OF A MINIMAL AUXIN RESPONSE SYSTEM. JRNL REF NAT.PLANTS V. 6 473 2020 JRNL REFN ESSN 2055-0278 JRNL PMID 32415296 JRNL DOI 10.1038/S41477-020-0662-Y REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.KATO,S.K.MUTTE,H.SUZUKI,I.CRESPO,S.DAS,T.RADOEVA, REMARK 1 AUTH 2 M.FONTANA,Y.YOSHITAKE,E.HAINIWA,W.VAN DEN BERG,S.LINDHOUD, REMARK 1 AUTH 3 J.HOHLBEIN,J.W.BORST,D.R.BOER,R.NISHIHAMA,T.KOHCHI, REMARK 1 AUTH 4 K.ISHIZAK,D.WEIJERS REMARK 1 TITL DESIGN PRINCIPLES OF A MINIMAL AUXIN RESPONSE SYSTEM REMARK 1 REF NAT.PLANTS 2020 REMARK 1 REFN ESSN 2055-0278 REMARK 1 DOI 10.1101/760876 REMARK 2 REMARK 2 RESOLUTION. 2.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 73.5 REMARK 3 NUMBER OF REFLECTIONS : 14014 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.480 REMARK 3 FREE R VALUE TEST SET COUNT : 768 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 29.2000 - 5.0500 0.99 3630 211 0.1811 0.2417 REMARK 3 2 5.0500 - 4.0100 0.99 3587 197 0.2089 0.2711 REMARK 3 3 4.0100 - 3.5100 0.91 3280 195 0.2710 0.3472 REMARK 3 4 3.5100 - 3.1900 0.56 2006 129 0.3120 0.3765 REMARK 3 5 3.1900 - 2.9600 0.21 743 36 0.3918 0.4793 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) : 0.486 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.334 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 101.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 112.7 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 : 0.013 6128 REMARK 3 ANGLE : 1.451 8509 REMARK 3 CHIRALITY : 0.075 924 REMARK 3 PLANARITY : 0.009 957 REMARK 3 DIHEDRAL : 19.992 3548 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 32.1062 56.7471 16.8740 REMARK 3 T TENSOR REMARK 3 T11: 0.6896 T22: 0.3493 REMARK 3 T33: 0.4828 T12: 0.0584 REMARK 3 T13: -0.0117 T23: 0.0234 REMARK 3 L TENSOR REMARK 3 L11: 2.4604 L22: 0.7380 REMARK 3 L33: 0.4317 L12: -0.2650 REMARK 3 L13: 0.4808 L23: 0.0863 REMARK 3 S TENSOR REMARK 3 S11: -0.3002 S12: -0.4278 S13: -0.2253 REMARK 3 S21: 0.1578 S22: 0.2119 S23: 0.0584 REMARK 3 S31: -0.2393 S32: -0.1240 S33: 0.1104 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 24 THROUGH 63 OR REMARK 3 RESID 69 THROUGH 108 OR RESID 126 THROUGH REMARK 3 304 OR RESID 307 THROUGH 360)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 24 THROUGH 232 OR REMARK 3 RESID 239 THROUGH 360)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'C' AND (RESID 0 THROUGH 8 OR REMARK 3 RESID 12 THROUGH 20)) REMARK 3 SELECTION : (CHAIN 'D' AND (RESID 0 THROUGH 8 OR REMARK 3 RESID 12 THROUGH 20)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6SDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292103412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97919 REMARK 200 MONOCHROMATOR : CHANNEL CUT SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14035 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.960 REMARK 200 RESOLUTION RANGE LOW (A) : 29.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 5.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 1.64100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: 4LDX REMARK 200 REMARK 200 REMARK: CUBE-SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: REQUIRED AMOUNT OF DNA TO 2:1 REMARK 280 (PROTEIN:DNA) STOICHIOMETRY WAS DILUTED IN [20 MM TRIS (PH8.0), REMARK 280 500 MM NACL] AND PROTEIN WAS ADDED TO FINAL CONCENTRATION OF 5 REMARK 280 MG/ML. CRYSTALS OF MPARF2-DBD:DNA WERE OBTAINED IN 0.2 M SODIUM REMARK 280 FORMATE, 20% W/V POLYETHYLENE GLYCOL 3,350 BY THE SITTING-DROP REMARK 280 VAPOR-DIFFUSION METHOD AT 18 DEG. C, IN DROPS OF 1 UL + 1 UL REMARK 280 (PROTEIN:RESERVOIR). CUBE-SHAPED CRYSTALS APPEARED IN LESS THAN REMARK 280 A WEEK. CRYO-COOLING IN LIQUID NITROGEN WAS CARRIED OUT USING A REMARK 280 CRYO-PROTECTING SOLUTION CONTAINING RESERVOIR SOLUTION REMARK 280 SUPPLEMENTED WITH 10% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 81.38400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 81.38400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.68000 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 GLN A 5 REMARK 465 LEU A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 SER A 9 REMARK 465 HIS A 10 REMARK 465 THR A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 SER A 14 REMARK 465 ASN A 15 REMARK 465 VAL A 16 REMARK 465 SER A 17 REMARK 465 VAL A 18 REMARK 465 ALA A 19 REMARK 465 GLY A 20 REMARK 465 ASP A 21 REMARK 465 ASP A 22 REMARK 465 GLY A 23 REMARK 465 HIS A 109 REMARK 465 GLU A 110 REMARK 465 ASP A 111 REMARK 465 SER A 112 REMARK 465 SER A 113 REMARK 465 ASP A 114 REMARK 465 CYS A 115 REMARK 465 ALA A 116 REMARK 465 GLU A 117 REMARK 465 PRO A 118 REMARK 465 PRO A 119 REMARK 465 PRO A 120 REMARK 465 PRO A 121 REMARK 465 GLN A 233 REMARK 465 GLN A 234 REMARK 465 GLN A 235 REMARK 465 LEU A 236 REMARK 465 GLN A 237 REMARK 465 PRO A 238 REMARK 465 SER A 361 REMARK 465 TYR A 362 REMARK 465 SER A 363 REMARK 465 GLN A 364 REMARK 465 SER A 365 REMARK 465 MET A 366 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 GLN B 5 REMARK 465 LEU B 6 REMARK 465 ALA B 7 REMARK 465 THR B 8 REMARK 465 SER B 9 REMARK 465 HIS B 10 REMARK 465 THR B 11 REMARK 465 ALA B 12 REMARK 465 ALA B 13 REMARK 465 SER B 14 REMARK 465 ASN B 15 REMARK 465 VAL B 16 REMARK 465 SER B 17 REMARK 465 VAL B 18 REMARK 465 ALA B 19 REMARK 465 GLY B 20 REMARK 465 ASP B 21 REMARK 465 ASP B 22 REMARK 465 GLY B 23 REMARK 465 GLU B 64 REMARK 465 LEU B 65 REMARK 465 ASP B 66 REMARK 465 ALA B 67 REMARK 465 GLN B 68 REMARK 465 HIS B 109 REMARK 465 GLU B 110 REMARK 465 ASP B 111 REMARK 465 SER B 112 REMARK 465 SER B 113 REMARK 465 ASP B 114 REMARK 465 CYS B 115 REMARK 465 ALA B 116 REMARK 465 GLU B 117 REMARK 465 PRO B 118 REMARK 465 PRO B 119 REMARK 465 PRO B 120 REMARK 465 PRO B 121 REMARK 465 PRO B 122 REMARK 465 LYS B 123 REMARK 465 ARG B 124 REMARK 465 LYS B 125 REMARK 465 GLU B 305 REMARK 465 ASP B 306 REMARK 465 TYR B 362 REMARK 465 SER B 363 REMARK 465 GLN B 364 REMARK 465 SER B 365 REMARK 465 MET B 366 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 B 297 OD2 ASP B 340 2.07 REMARK 500 OD1 ASP B 25 NH1 ARG B 224 2.13 REMARK 500 NE2 HIS B 141 O6 DG D 6 2.17 REMARK 500 OE2 GLU B 27 N SER B 126 2.18 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 C1' DT C 1 N1 -0.104 REMARK 500 DC C 18 O3' DC C 18 C3' -0.041 REMARK 500 DT D 1 C1' DT D 1 N1 -0.086 REMARK 500 DG D 2 O3' DG D 2 C3' -0.037 REMARK 500 DC D 7 O3' DC D 7 C3' 0.089 REMARK 500 DG D 16 O3' DG D 16 C3' -0.045 REMARK 500 DC D 18 O3' DC D 18 C3' -0.038 REMARK 500 DA D 19 O3' DA D 19 C3' -0.059 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 CYS A 154 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 DT C 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT C 10 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 1 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG D 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC D 18 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA D 19 O4' - C1' - N9 ANGL. DEV. = 2.6 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 ALA A 33 -72.17 -64.85 REMARK 500 LYS A 123 -112.80 58.15 REMARK 500 THR A 195 -68.94 -121.47 REMARK 500 ASN A 220 -5.79 -59.86 REMARK 500 LYS A 301 67.04 -103.90 REMARK 500 ARG A 310 87.53 54.81 REMARK 500 ASP A 321 109.01 -59.82 REMARK 500 ALA A 325 -71.47 -62.39 REMARK 500 GLU A 341 70.84 40.20 REMARK 500 SER A 343 62.52 -114.71 REMARK 500 ASP B 25 66.88 60.40 REMARK 500 ALA B 33 -70.07 -63.86 REMARK 500 ARG B 127 93.36 50.82 REMARK 500 THR B 195 -76.06 -116.09 REMARK 500 ARG B 217 -75.65 -104.26 REMARK 500 PRO B 280 128.86 -36.84 REMARK 500 GLU B 303 -77.29 -87.60 REMARK 500 GLU B 341 68.64 -103.15 REMARK 500 SER B 343 -95.95 -69.88 REMARK 500 SER B 344 23.80 -67.44 REMARK 500 SER B 345 52.40 34.25 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6SDG A 1 358 UNP A0A0K2QVG1_MARPO DBREF2 6SDG A A0A0K2QVG1 38 395 DBREF1 6SDG B 1 358 UNP A0A0K2QVG1_MARPO DBREF2 6SDG B A0A0K2QVG1 38 395 DBREF 6SDG C 0 20 PDB 6SDG 6SDG 0 20 DBREF 6SDG D 0 20 PDB 6SDG 6SDG 0 20 SEQADV 6SDG GLY A 359 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG ASN A 360 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG SER A 361 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG TYR A 362 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG SER A 363 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG GLN A 364 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG SER A 365 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG MET A 366 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG GLY B 359 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG ASN B 360 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG SER B 361 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG TYR B 362 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG SER B 363 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG GLN B 364 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG SER B 365 UNP A0A0K2QVG EXPRESSION TAG SEQADV 6SDG MET B 366 UNP A0A0K2QVG EXPRESSION TAG SEQRES 1 A 366 MET ALA SER ARG GLN LEU ALA THR SER HIS THR ALA ALA SEQRES 2 A 366 SER ASN VAL SER VAL ALA GLY ASP ASP GLY ILE ASP ALA SEQRES 3 A 366 GLU LEU TRP TYR ALA CYS ALA GLY PRO GLN LYS ALA LEU SEQRES 4 A 366 PRO PRO VAL GLY SER VAL VAL ALA TYR LEU PRO GLN GLY SEQRES 5 A 366 HIS ILE GLU GLN VAL ALA SER PHE ASN ASN GLN GLU LEU SEQRES 6 A 366 ASP ALA GLN ILE PRO ARG TYR ASN LEU PRO ALA VAL ILE SEQRES 7 A 366 PRO CYS MET LEU ASN ASP ILE GLN LEU SER ALA ASP PRO SEQRES 8 A 366 ASP SER ASP GLU VAL TYR ALA THR LEU THR LEU CYS PRO SEQRES 9 A 366 MET SER GLU GLN HIS GLU ASP SER SER ASP CYS ALA GLU SEQRES 10 A 366 PRO PRO PRO PRO PRO LYS ARG LYS SER ARG SER PHE THR SEQRES 11 A 366 LYS THR LEU THR VAL SER ASP THR SER THR HIS GLY GLY SEQRES 12 A 366 PHE SER VAL PRO ARG ARG ALA ALA ASP ASP CYS LEU PRO SEQRES 13 A 366 LYS LEU ASP MET SER LEU ASN PRO PRO ASN GLN GLU LEU SEQRES 14 A 366 VAL ALA LYS ASP LEU HIS GLY ASN GLU TRP ARG PHE ARG SEQRES 15 A 366 HIS ILE PHE ARG GLY GLN PRO LYS ARG HIS LEU LEU THR SEQRES 16 A 366 THR GLY TRP SER VAL PHE VAL SER GLN LYS ARG LEU VAL SEQRES 17 A 366 ALA GLY ASP ALA VAL LEU PHE LEU ARG GLY GLU ASN GLY SEQRES 18 A 366 GLN LEU ARG VAL GLY VAL ARG ARG ALA PRO ARG GLN GLN SEQRES 19 A 366 GLN LEU GLN PRO LYS VAL LEU THR SER PRO THR MET HIS SEQRES 20 A 366 ILE GLY VAL LEU ALA ALA ALA ALA HIS ALA ALA THR GLU SEQRES 21 A 366 LYS SER ARG PHE SER LEU ILE TYR ASN PRO ARG SER CYS SEQRES 22 A 366 PRO SER GLU PHE VAL ILE PRO TYR SER LYS TYR LEU LYS SEQRES 23 A 366 ALA VAL LYS SER ASN PHE ASN VAL GLY GLN ARG PHE LYS SEQRES 24 A 366 MET LYS PHE GLU SER GLU ASP PRO SER ASP ARG ARG HIS SEQRES 25 A 366 THR GLY THR ILE THR GLY ILE CYS ASP PHE ASP PRO ALA SEQRES 26 A 366 ARG TRP PRO GLY SER GLU TRP ARG SER LEU GLN VAL ASN SEQRES 27 A 366 TRP ASP GLU SER SER SER SER GLU ARG GLN GLU ARG VAL SEQRES 28 A 366 SER PRO TRP GLU VAL GLU PRO GLY ASN SER TYR SER GLN SEQRES 29 A 366 SER MET SEQRES 1 B 366 MET ALA SER ARG GLN LEU ALA THR SER HIS THR ALA ALA SEQRES 2 B 366 SER ASN VAL SER VAL ALA GLY ASP ASP GLY ILE ASP ALA SEQRES 3 B 366 GLU LEU TRP TYR ALA CYS ALA GLY PRO GLN LYS ALA LEU SEQRES 4 B 366 PRO PRO VAL GLY SER VAL VAL ALA TYR LEU PRO GLN GLY SEQRES 5 B 366 HIS ILE GLU GLN VAL ALA SER PHE ASN ASN GLN GLU LEU SEQRES 6 B 366 ASP ALA GLN ILE PRO ARG TYR ASN LEU PRO ALA VAL ILE SEQRES 7 B 366 PRO CYS MET LEU ASN ASP ILE GLN LEU SER ALA ASP PRO SEQRES 8 B 366 ASP SER ASP GLU VAL TYR ALA THR LEU THR LEU CYS PRO SEQRES 9 B 366 MET SER GLU GLN HIS GLU ASP SER SER ASP CYS ALA GLU SEQRES 10 B 366 PRO PRO PRO PRO PRO LYS ARG LYS SER ARG SER PHE THR SEQRES 11 B 366 LYS THR LEU THR VAL SER ASP THR SER THR HIS GLY GLY SEQRES 12 B 366 PHE SER VAL PRO ARG ARG ALA ALA ASP ASP CYS LEU PRO SEQRES 13 B 366 LYS LEU ASP MET SER LEU ASN PRO PRO ASN GLN GLU LEU SEQRES 14 B 366 VAL ALA LYS ASP LEU HIS GLY ASN GLU TRP ARG PHE ARG SEQRES 15 B 366 HIS ILE PHE ARG GLY GLN PRO LYS ARG HIS LEU LEU THR SEQRES 16 B 366 THR GLY TRP SER VAL PHE VAL SER GLN LYS ARG LEU VAL SEQRES 17 B 366 ALA GLY ASP ALA VAL LEU PHE LEU ARG GLY GLU ASN GLY SEQRES 18 B 366 GLN LEU ARG VAL GLY VAL ARG ARG ALA PRO ARG GLN GLN SEQRES 19 B 366 GLN LEU GLN PRO LYS VAL LEU THR SER PRO THR MET HIS SEQRES 20 B 366 ILE GLY VAL LEU ALA ALA ALA ALA HIS ALA ALA THR GLU SEQRES 21 B 366 LYS SER ARG PHE SER LEU ILE TYR ASN PRO ARG SER CYS SEQRES 22 B 366 PRO SER GLU PHE VAL ILE PRO TYR SER LYS TYR LEU LYS SEQRES 23 B 366 ALA VAL LYS SER ASN PHE ASN VAL GLY GLN ARG PHE LYS SEQRES 24 B 366 MET LYS PHE GLU SER GLU ASP PRO SER ASP ARG ARG HIS SEQRES 25 B 366 THR GLY THR ILE THR GLY ILE CYS ASP PHE ASP PRO ALA SEQRES 26 B 366 ARG TRP PRO GLY SER GLU TRP ARG SER LEU GLN VAL ASN SEQRES 27 B 366 TRP ASP GLU SER SER SER SER GLU ARG GLN GLU ARG VAL SEQRES 28 B 366 SER PRO TRP GLU VAL GLU PRO GLY ASN SER TYR SER GLN SEQRES 29 B 366 SER MET SEQRES 1 C 21 DT DT DG DT DC DG DG DC DG DA DT DT DC SEQRES 2 C 21 DG DC DC DG DA DC DA DA SEQRES 1 D 21 DT DT DG DT DC DG DG DC DG DA DA DT DC SEQRES 2 D 21 DG DC DC DG DA DC DA DA HELIX 1 AA1 ASP A 25 GLY A 34 1 10 HELIX 2 AA2 LEU A 49 ASN A 61 1 13 HELIX 3 AA3 THR A 134 SER A 139 1 6 HELIX 4 AA4 PRO A 147 CYS A 154 1 8 HELIX 5 AA5 GLY A 197 LYS A 205 1 9 HELIX 6 AA6 THR A 242 GLU A 260 1 19 HELIX 7 AA7 TYR A 281 SER A 290 1 10 HELIX 8 AA8 ASP B 25 GLY B 34 1 10 HELIX 9 AA9 LEU B 49 ASN B 61 1 13 HELIX 10 AB1 THR B 134 SER B 139 1 6 HELIX 11 AB2 PRO B 147 CYS B 154 1 8 HELIX 12 AB3 GLY B 197 LYS B 205 1 9 HELIX 13 AB4 THR B 242 GLU B 260 1 19 HELIX 14 AB5 TYR B 281 SER B 290 1 10 HELIX 15 AB6 SER B 352 VAL B 356 5 5 SHEET 1 AA1 5 PHE A 264 TYR A 268 0 SHEET 2 AA1 5 VAL A 96 PRO A 104 -1 N LEU A 102 O PHE A 264 SHEET 3 AA1 5 ILE A 78 ALA A 89 -1 N MET A 81 O CYS A 103 SHEET 4 AA1 5 VAL A 45 TYR A 48 -1 N TYR A 48 O ILE A 78 SHEET 5 AA1 5 VAL A 278 PRO A 280 -1 O ILE A 279 N ALA A 47 SHEET 1 AA2 7 SER A 128 THR A 132 0 SHEET 2 AA2 7 ALA A 212 ARG A 217 -1 O VAL A 213 N LYS A 131 SHEET 3 AA2 7 LEU A 223 ARG A 228 -1 O ARG A 224 N LEU A 216 SHEET 4 AA2 7 ASN A 166 LYS A 172 1 N LYS A 172 O VAL A 225 SHEET 5 AA2 7 GLU A 178 ARG A 186 -1 O PHE A 181 N LEU A 169 SHEET 6 AA2 7 ARG A 191 LEU A 194 -1 O ARG A 191 N ARG A 186 SHEET 7 AA2 7 PHE A 144 VAL A 146 -1 N PHE A 144 O LEU A 194 SHEET 1 AA3 5 ARG A 350 VAL A 351 0 SHEET 2 AA3 5 LEU A 335 TRP A 339 -1 N LEU A 335 O VAL A 351 SHEET 3 AA3 5 HIS A 312 ILE A 319 -1 N GLY A 318 O GLN A 336 SHEET 4 AA3 5 ARG A 297 MET A 300 -1 N PHE A 298 O GLY A 314 SHEET 5 AA3 5 GLU A 357 PRO A 358 -1 O GLU A 357 N LYS A 299 SHEET 1 AA4 5 PHE B 264 TYR B 268 0 SHEET 2 AA4 5 VAL B 96 PRO B 104 -1 N ALA B 98 O TYR B 268 SHEET 3 AA4 5 ILE B 78 ALA B 89 -1 N ASN B 83 O THR B 101 SHEET 4 AA4 5 VAL B 45 TYR B 48 -1 N TYR B 48 O ILE B 78 SHEET 5 AA4 5 VAL B 278 PRO B 280 -1 O ILE B 279 N ALA B 47 SHEET 1 AA5 3 SER B 128 THR B 132 0 SHEET 2 AA5 3 ALA B 212 LEU B 216 -1 O VAL B 213 N LYS B 131 SHEET 3 AA5 3 ARG B 224 ARG B 228 -1 O ARG B 224 N LEU B 216 SHEET 1 AA6 4 PHE B 144 VAL B 146 0 SHEET 2 AA6 4 ARG B 191 LEU B 194 -1 O HIS B 192 N VAL B 146 SHEET 3 AA6 4 GLU B 178 ARG B 186 -1 N ILE B 184 O LEU B 193 SHEET 4 AA6 4 ASN B 166 LYS B 172 -1 N LEU B 169 O PHE B 181 SHEET 1 AA7 5 ARG B 350 VAL B 351 0 SHEET 2 AA7 5 LEU B 335 TRP B 339 -1 N LEU B 335 O VAL B 351 SHEET 3 AA7 5 HIS B 312 ILE B 319 -1 N GLY B 318 O GLN B 336 SHEET 4 AA7 5 ARG B 297 MET B 300 -1 N PHE B 298 O GLY B 314 SHEET 5 AA7 5 GLU B 357 PRO B 358 -1 O GLU B 357 N LYS B 299 CISPEP 1 ASN A 163 PRO A 164 0 5.35 CISPEP 2 GLN A 188 PRO A 189 0 12.66 CISPEP 3 GLN B 188 PRO B 189 0 13.72 CRYST1 162.768 79.360 79.767 90.00 116.93 90.00 C 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 0.006144 0.000000 0.003121 0.00000 SCALE2 0.000000 0.012601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014061 0.00000