HEADER PLANT PROTEIN 01-DEC-19 6TL4 TITLE PHOTOSENSORY MODULE (PAS-GAF-PHY) OF GLYCINE MAX PHYB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYTOCHROME; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 GENE: 100794865, GLYMA_15G140000; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCDFDUET-1 KEYWDS PHYTOCHROME, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.NAGANO,K.GUAN,S.M.SHENKUTIE,J.E.HUGHES REVDAT 4 24-JAN-24 6TL4 1 REMARK REVDAT 3 27-MAY-20 6TL4 1 JRNL REVDAT 2 13-MAY-20 6TL4 1 JRNL REVDAT 1 06-MAY-20 6TL4 0 JRNL AUTH S.NAGANO,K.GUAN,S.M.SHENKUTIE,C.FEILER,M.WEISS,A.KRASKOV, JRNL AUTH 2 D.BUHRKE,P.HILDEBRANDT,J.HUGHES JRNL TITL STRUCTURAL INSIGHTS INTO PHOTOACTIVATION AND SIGNALLING IN JRNL TITL 2 PLANT PHYTOCHROMES. JRNL REF NAT.PLANTS V. 6 581 2020 JRNL REFN ESSN 2055-0278 JRNL PMID 32366982 JRNL DOI 10.1038/S41477-020-0638-Y REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 30475 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1550 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 47.1700 - 6.4500 0.99 2838 127 0.2106 0.2177 REMARK 3 2 6.4400 - 5.1200 1.00 2704 125 0.2594 0.3262 REMARK 3 3 5.1200 - 4.4700 1.00 2704 117 0.2175 0.1868 REMARK 3 4 4.4700 - 4.0600 1.00 2620 154 0.2290 0.2856 REMARK 3 5 4.0600 - 3.7700 1.00 2616 149 0.2551 0.2985 REMARK 3 6 3.7700 - 3.5500 1.00 2573 168 0.2800 0.2898 REMARK 3 7 3.5500 - 3.3700 1.00 2622 149 0.3279 0.3540 REMARK 3 8 3.3700 - 3.2300 0.99 2571 151 0.3386 0.3361 REMARK 3 9 3.2200 - 3.1000 0.99 2575 134 0.3623 0.3710 REMARK 3 10 3.1000 - 2.9900 0.99 2582 144 0.3790 0.4009 REMARK 3 11 2.9900 - 2.9000 0.96 2520 132 0.4569 0.4702 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 33.452 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 85.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 121.8 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 : 0.009 3919 REMARK 3 ANGLE : 1.392 5330 REMARK 3 CHIRALITY : 0.067 604 REMARK 3 PLANARITY : 0.008 683 REMARK 3 DIHEDRAL : 18.324 575 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 345 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.4619 -17.6252 25.0094 REMARK 3 T TENSOR REMARK 3 T11: 1.1081 T22: 0.7644 REMARK 3 T33: 0.7557 T12: 0.3269 REMARK 3 T13: 0.0304 T23: -0.0314 REMARK 3 L TENSOR REMARK 3 L11: 2.4887 L22: 4.0068 REMARK 3 L33: 5.5756 L12: 0.4710 REMARK 3 L13: -0.7998 L23: 2.1925 REMARK 3 S TENSOR REMARK 3 S11: 0.1725 S12: -0.0133 S13: 0.4831 REMARK 3 S21: -0.2130 S22: 0.1692 S23: -0.2176 REMARK 3 S31: -1.3825 S32: 0.4453 S33: -0.3330 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 346 THROUGH 448 OR RESID 700 REMARK 3 THROUGH 702 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.0337 -34.8574 24.4979 REMARK 3 T TENSOR REMARK 3 T11: 1.2376 T22: 0.8941 REMARK 3 T33: 0.6604 T12: 0.4458 REMARK 3 T13: -0.0162 T23: -0.0592 REMARK 3 L TENSOR REMARK 3 L11: 1.8894 L22: 4.5990 REMARK 3 L33: 0.4971 L12: -2.3540 REMARK 3 L13: -0.7393 L23: 1.6153 REMARK 3 S TENSOR REMARK 3 S11: -0.2258 S12: -0.4026 S13: 0.1956 REMARK 3 S21: 0.4268 S22: 0.6491 S23: -0.1552 REMARK 3 S31: -0.0553 S32: 0.3391 S33: -0.3300 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 449 THROUGH 618 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4328 -61.7191 13.1903 REMARK 3 T TENSOR REMARK 3 T11: 1.1066 T22: 1.1894 REMARK 3 T33: 0.6803 T12: 0.5137 REMARK 3 T13: 0.0555 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 1.0347 L22: 4.4626 REMARK 3 L33: 4.4848 L12: -1.0452 REMARK 3 L13: 0.4483 L23: -1.4712 REMARK 3 S TENSOR REMARK 3 S11: 0.2880 S12: 0.3518 S13: -0.0900 REMARK 3 S21: -0.5820 S22: -0.4302 S23: -0.7506 REMARK 3 S31: 1.3684 S32: 0.9825 S33: 0.1941 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 6TL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105646. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.23800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 19.90 REMARK 200 R MERGE FOR SHELL (I) : 5.83800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 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: 4OUR REMARK 200 REMARK 200 REMARK: HEXAGONAL BIPYRAMID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM MES, 200MM KSCN, 200MM LICL2, 1% REMARK 280 W/V GAMMA-PGA, 3% W/V PEG3350, PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 283.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.30600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 148.61200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 148.61200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.30600 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 83 REMARK 465 ALA A 84 REMARK 465 VAL A 85 REMARK 465 THR A 86 REMARK 465 SER A 87 REMARK 465 GLU A 88 REMARK 465 SER A 89 REMARK 465 VAL A 90 REMARK 465 PRO A 91 REMARK 465 GLU A 92 REMARK 465 GLN A 93 REMARK 465 GLN A 94 REMARK 465 THR A 138 REMARK 465 PRO A 139 REMARK 465 GLN A 140 REMARK 465 SER A 141 REMARK 465 VAL A 142 REMARK 465 PRO A 143 REMARK 465 SER A 144 REMARK 465 LEU A 145 REMARK 465 ASP A 146 REMARK 465 ASP A 147 REMARK 465 LYS A 148 REMARK 465 ASN A 149 REMARK 465 ASP A 150 REMARK 465 ALA A 151 REMARK 465 ALA A 152 REMARK 465 GLU A 218 REMARK 465 ASP A 219 REMARK 465 PRO A 220 REMARK 465 ASN A 376 REMARK 465 ASP A 377 REMARK 465 GLU A 378 REMARK 465 GLU A 379 REMARK 465 GLY A 380 REMARK 465 VAL A 381 REMARK 465 GLY A 382 REMARK 465 GLY A 383 REMARK 465 ARG A 384 REMARK 465 THR A 385 REMARK 465 HIS A 619 REMARK 465 HIS A 620 REMARK 465 HIS A 621 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 A 101 CG CD CE NZ REMARK 470 ARG A 104 CG CD NE CZ NH1 NH2 REMARK 470 MET A 114 CG SD CE REMARK 470 ARG A 123 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 125 CG CD1 CD2 REMARK 470 PHE A 153 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 195 CG CD CE NZ REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 292 CG CD OE1 OE2 REMARK 470 ARG A 329 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 332 CG CD OE1 NE2 REMARK 470 LYS A 435 CG CD CE NZ REMARK 470 GLN A 459 CG CD OE1 NE2 REMARK 470 SER A 460 OG REMARK 470 ARG A 504 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 505 CG OD1 OD2 REMARK 470 SER A 506 OG REMARK 470 THR A 507 OG1 CG2 REMARK 470 ASP A 516 CG OD1 OD2 REMARK 470 SER A 524 OG REMARK 470 THR A 538 OG1 CG2 REMARK 470 GLU A 539 CG CD OE1 OE2 REMARK 470 LYS A 540 CG CD CE NZ REMARK 470 LYS A 560 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 OE1 GLU A 119 NH2 ARG A 203 1.42 REMARK 500 CD GLU A 119 NH2 ARG A 203 1.77 REMARK 500 OE2 GLU A 119 NH2 ARG A 203 1.82 REMARK 500 OD1 ASP A 267 ND1 HIS A 397 2.06 REMARK 500 OE1 GLU A 119 CZ ARG A 203 2.18 REMARK 500 NH1 ARG A 160 OE1 GLU A 172 2.18 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 CE LYS A 232 OE1 GLN A 441 6455 0.99 REMARK 500 CE LYS A 232 CD GLN A 441 6455 1.25 REMARK 500 CD LYS A 232 OE1 GLN A 441 6455 1.46 REMARK 500 NZ LYS A 232 OE1 GLN A 441 6455 1.61 REMARK 500 NZ LYS A 232 CD GLN A 441 6455 1.79 REMARK 500 CE LYS A 232 NE2 GLN A 441 6455 1.85 REMARK 500 NZ LYS A 232 CG GLN A 441 6455 1.93 REMARK 500 NZ LYS A 232 CB GLN A 441 6455 1.97 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 LEU A 100 CA - CB - CG ANGL. DEV. = 21.2 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 TYR A 98 -16.75 72.96 REMARK 500 ASP A 118 143.07 -37.18 REMARK 500 ALA A 126 134.21 -172.23 REMARK 500 TYR A 127 -149.44 -121.86 REMARK 500 LEU A 155 127.58 -174.59 REMARK 500 ILE A 180 -51.65 -28.48 REMARK 500 SER A 181 -33.76 -39.17 REMARK 500 SER A 193 -36.45 -133.54 REMARK 500 ILE A 204 -167.08 -118.54 REMARK 500 SER A 243 49.95 -79.79 REMARK 500 ASP A 248 74.80 -161.99 REMARK 500 SER A 399 -169.15 -104.27 REMARK 500 GLN A 477 60.85 65.04 REMARK 500 ALA A 515 -73.69 -58.67 REMARK 500 CYS A 530 -33.10 -132.67 REMARK 500 PHE A 578 17.72 -143.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYC A 700 DBREF 6TL4 A 85 616 UNP I1MGE5 I1MGE5_SOYBN 85 616 SEQADV 6TL4 MET A 83 UNP I1MGE5 INITIATING METHIONINE SEQADV 6TL4 ALA A 84 UNP I1MGE5 EXPRESSION TAG SEQADV 6TL4 HIS A 617 UNP I1MGE5 EXPRESSION TAG SEQADV 6TL4 HIS A 618 UNP I1MGE5 EXPRESSION TAG SEQADV 6TL4 HIS A 619 UNP I1MGE5 EXPRESSION TAG SEQADV 6TL4 HIS A 620 UNP I1MGE5 EXPRESSION TAG SEQADV 6TL4 HIS A 621 UNP I1MGE5 EXPRESSION TAG SEQRES 1 A 539 MET ALA VAL THR SER GLU SER VAL PRO GLU GLN GLN ILE SEQRES 2 A 539 THR ALA TYR LEU LEU LYS ILE GLN ARG GLY GLY PHE ILE SEQRES 3 A 539 GLN PRO PHE GLY SER MET ILE ALA VAL ASP GLU PRO SER SEQRES 4 A 539 PHE ARG ILE LEU ALA TYR SER ASP ASN ALA ARG ASP MET SEQRES 5 A 539 LEU GLY ILE THR PRO GLN SER VAL PRO SER LEU ASP ASP SEQRES 6 A 539 LYS ASN ASP ALA ALA PHE ALA LEU GLY THR ASP ILE ARG SEQRES 7 A 539 THR LEU PHE THR HIS SER SER ALA VAL LEU LEU GLU LYS SEQRES 8 A 539 ALA PHE SER ALA ARG GLU ILE SER LEU MET ASN PRO ILE SEQRES 9 A 539 TRP ILE HIS SER ARG THR SER GLY LYS PRO PHE TYR GLY SEQRES 10 A 539 ILE LEU HIS ARG ILE ASP VAL GLY ILE VAL ILE ASP LEU SEQRES 11 A 539 GLU PRO ALA ARG THR GLU ASP PRO ALA LEU SER ILE ALA SEQRES 12 A 539 GLY ALA VAL GLN SER GLN LYS LEU ALA VAL ARG ALA ILE SEQRES 13 A 539 SER GLN LEU GLN SER LEU PRO GLY GLY ASP VAL LYS LEU SEQRES 14 A 539 LEU CYS ASP THR VAL VAL GLU SER VAL ARG GLU LEU THR SEQRES 15 A 539 GLY TYR ASP ARG VAL MET VAL TYR ARG PHE HIS GLU ASP SEQRES 16 A 539 GLU HIS GLY GLU VAL VAL ALA GLU THR LYS ARG PRO ASP SEQRES 17 A 539 LEU GLU PRO TYR ILE GLY LEU HIS TYR PRO ALA THR ASP SEQRES 18 A 539 ILE PRO GLN ALA SER ARG PHE LEU PHE LYS GLN ASN ARG SEQRES 19 A 539 VAL ARG MET ILE VAL ASP CYS HIS ALA SER ALA VAL ARG SEQRES 20 A 539 VAL VAL GLN ASP GLU ALA LEU VAL GLN PRO LEU CYS LEU SEQRES 21 A 539 VAL GLY SER THR LEU ARG ALA PRO HIS GLY CYS HIS ALA SEQRES 22 A 539 GLN TYR MET ALA ASN MET GLY SER THR ALA SER LEU VAL SEQRES 23 A 539 MET ALA VAL ILE ILE ASN GLY ASN ASP GLU GLU GLY VAL SEQRES 24 A 539 GLY GLY ARG THR SER MET ARG LEU TRP GLY LEU VAL VAL SEQRES 25 A 539 CYS HIS HIS THR SER ALA ARG CYS ILE PRO PHE PRO LEU SEQRES 26 A 539 ARG TYR ALA CYS GLU PHE LEU MET GLN ALA PHE GLY LEU SEQRES 27 A 539 GLN LEU ASN MET GLU LEU GLN LEU ALA ALA GLN SER LEU SEQRES 28 A 539 GLU LYS ARG VAL LEU ARG THR GLN THR LEU LEU CYS ASP SEQRES 29 A 539 MET LEU LEU ARG ASP SER PRO THR GLY ILE VAL THR GLN SEQRES 30 A 539 SER PRO SER ILE MET ASP LEU VAL LYS CYS ASP GLY ALA SEQRES 31 A 539 ALA LEU TYR TYR GLN GLY ASN TYR TYR PRO LEU GLY VAL SEQRES 32 A 539 THR PRO THR GLU ALA GLN ILE ARG ASP ILE ILE GLU TRP SEQRES 33 A 539 LEU LEU ALA PHE HIS ARG ASP SER THR GLY LEU SER THR SEQRES 34 A 539 ASP SER LEU ALA ASP ALA GLY TYR PRO GLY ALA ALA SER SEQRES 35 A 539 LEU GLY ASP ALA VAL CYS GLY MET ALA VAL ALA TYR ILE SEQRES 36 A 539 THR GLU LYS ASP PHE LEU PHE TRP PHE ARG SER HIS THR SEQRES 37 A 539 ALA LYS GLU ILE LYS TRP GLY GLY ALA LYS HIS HIS PRO SEQRES 38 A 539 GLU ASP LYS ASP ASP GLY GLN ARG MET HIS PRO ARG SER SEQRES 39 A 539 SER PHE LYS ALA PHE LEU GLU VAL VAL LYS SER ARG SER SEQRES 40 A 539 LEU PRO TRP GLU ASN ALA GLU MET ASP ALA ILE HIS SER SEQRES 41 A 539 LEU GLN LEU ILE LEU ARG ASP SER PHE LYS ASP ALA GLU SEQRES 42 A 539 HIS HIS HIS HIS HIS HIS HET CYC A 700 43 HETNAM CYC PHYCOCYANOBILIN FORMUL 2 CYC C33 H40 N4 O6 FORMUL 3 HOH *2(H2 O) HELIX 1 AA1 TYR A 98 ARG A 104 1 7 HELIX 2 AA2 ASN A 130 GLY A 136 1 7 HELIX 3 AA3 ILE A 159 PHE A 163 5 5 HELIX 4 AA4 THR A 164 SER A 176 1 13 HELIX 5 AA5 GLU A 179 MET A 183 5 5 HELIX 6 AA6 SER A 223 SER A 243 1 21 HELIX 7 AA7 ASP A 248 GLY A 265 1 18 HELIX 8 AA8 PRO A 305 LYS A 313 1 9 HELIX 9 AA9 HIS A 351 GLY A 362 1 12 HELIX 10 AB1 PRO A 404 LEU A 449 1 46 HELIX 11 AB2 THR A 454 GLN A 459 1 6 HELIX 12 AB3 THR A 488 HIS A 503 1 16 HELIX 13 AB4 SER A 513 GLY A 518 1 6 HELIX 14 AB5 GLU A 593 HIS A 618 1 26 SHEET 1 AA1 2 PHE A 107 ILE A 108 0 SHEET 2 AA1 2 VAL A 328 ARG A 329 -1 O VAL A 328 N ILE A 108 SHEET 1 AA2 5 ILE A 124 ALA A 126 0 SHEET 2 AA2 5 SER A 113 VAL A 117 -1 N ALA A 116 O ALA A 126 SHEET 3 AA2 5 ILE A 208 PRO A 214 -1 O ILE A 208 N VAL A 117 SHEET 4 AA2 5 PRO A 196 ARG A 203 -1 N ILE A 200 O ASP A 211 SHEET 5 AA2 5 ILE A 186 HIS A 189 -1 N ILE A 188 O PHE A 197 SHEET 1 AA3 8 VAL A 317 ILE A 320 0 SHEET 2 AA3 8 ALA A 365 ILE A 373 -1 O VAL A 368 N ARG A 318 SHEET 3 AA3 8 ARG A 388 HIS A 397 -1 O HIS A 397 N ALA A 365 SHEET 4 AA3 8 ARG A 268 PHE A 274 -1 N ARG A 268 O HIS A 396 SHEET 5 AA3 8 GLY A 280 LYS A 287 -1 O VAL A 283 N VAL A 271 SHEET 6 AA3 8 LEU A 297 TYR A 299 -1 O TYR A 299 N GLY A 280 SHEET 7 AA3 8 LYS A 552 GLY A 557 1 O GLY A 557 N HIS A 298 SHEET 8 AA3 8 ALA A 580 VAL A 585 -1 O PHE A 581 N TRP A 556 SHEET 1 AA4 5 ASN A 479 GLY A 484 0 SHEET 2 AA4 5 GLY A 471 TYR A 476 -1 N ALA A 472 O LEU A 483 SHEET 3 AA4 5 ASP A 541 ARG A 547 -1 O PHE A 544 N ALA A 473 SHEET 4 AA4 5 GLY A 531 THR A 538 -1 N GLY A 531 O ARG A 547 SHEET 5 AA4 5 LEU A 509 THR A 511 -1 N THR A 511 O MET A 532 LINK SG CYS A 353 CAC CYC A 700 1555 1555 1.76 CISPEP 1 ASN A 184 PRO A 185 0 7.07 SITE 1 AC1 19 TYR A 98 MET A 270 THR A 302 ASP A 303 SITE 2 AC1 19 ILE A 304 PRO A 305 PHE A 312 ARG A 318 SITE 3 AC1 19 ARG A 348 PRO A 350 HIS A 351 CYS A 353 SITE 4 AC1 19 HIS A 354 TYR A 357 VAL A 368 HIS A 396 SITE 5 AC1 19 ARG A 571 HIS A 573 HOH A 801 CRYST1 102.269 102.269 222.918 90.00 90.00 120.00 P 31 2 1 6 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 0.009778 0.005645 0.000000 0.00000 SCALE2 0.000000 0.011291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004486 0.00000