HEADER PLANT PROTEIN 13-NOV-23 8R44 TITLE PAS-GAF BIDOMAIN OF GLYCINE MAX PHYTOCHROME A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYTOCHROME A-2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GMPHYA2; COMPND 5 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: PHYA2, GLYMA_20G090000; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PHYTOCHROME, PHYCOCYANOBILIN (PCB), PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.GUAN,S.NAGANO,J.HUGHES REVDAT 1 08-JAN-25 8R44 0 JRNL AUTH K.GUAN,S.NAGANO,J.HUGHES JRNL TITL STRUCTURE OF PLANT PHYTOCHROME A JRNL REF NAT COMMUN 2025 JRNL REFN ESSN 2041-1723 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0403 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 112680 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) : 0.175 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.767 REMARK 3 FREE R VALUE TEST SET COUNT : 5372 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7946 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 384 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4924 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 158 REMARK 3 SOLVENT ATOMS : 587 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06400 REMARK 3 B22 (A**2) : 0.00400 REMARK 3 B33 (A**2) : 0.04900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.12800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.154 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5202 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4966 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7032 ; 1.623 ; 1.681 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11474 ; 0.526 ; 1.573 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 622 ; 6.537 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 24 ; 8.465 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 874 ;16.062 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 788 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5774 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1080 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1039 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 54 ; 0.226 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2483 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 471 ; 0.197 ; 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): 2506 ; 2.884 ; 2.396 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2506 ; 2.882 ; 2.396 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3122 ; 4.613 ; 4.266 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3123 ; 4.613 ; 4.269 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2696 ; 4.037 ; 3.049 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2697 ; 4.038 ; 3.049 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3910 ; 6.258 ; 5.335 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3911 ; 6.257 ; 5.336 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 69 A 505 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3858 14.5836 22.5775 REMARK 3 T TENSOR REMARK 3 T11: 0.0168 T22: 0.0535 REMARK 3 T33: 0.0263 T12: -0.0187 REMARK 3 T13: 0.0087 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.7949 L22: 0.0392 REMARK 3 L33: 0.2228 L12: 0.0017 REMARK 3 L13: -0.0192 L23: -0.0224 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: -0.0581 S13: -0.0958 REMARK 3 S21: 0.0012 S22: 0.0104 S23: -0.0077 REMARK 3 S31: -0.0559 S32: 0.0337 S33: -0.0459 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 0.4983 2.0293 -6.1759 REMARK 3 T TENSOR REMARK 3 T11: 0.0185 T22: 0.0331 REMARK 3 T33: 0.0390 T12: -0.0155 REMARK 3 T13: 0.0203 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 0.0797 L22: 0.7239 REMARK 3 L33: 0.1913 L12: -0.0850 REMARK 3 L13: -0.0822 L23: -0.0710 REMARK 3 S TENSOR REMARK 3 S11: -0.0108 S12: 0.0448 S13: -0.0217 REMARK 3 S21: -0.0425 S22: 0.0149 S23: -0.0409 REMARK 3 S31: 0.0053 S32: -0.0581 S33: -0.0041 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 8R44 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1292134543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 40 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.896 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 : 112709 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 43.841 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12 M ETHYLENE GLYCOLS (0.3M REMARK 280 DIETHYLENE GLYCOL; 0.3M TRIETHYLENE GLYCOL; 0.3M TETRAETHYLENE REMARK 280 GLYCOL; 0.3M PENTAETHYLENE GLYCOL), 0.1 M TRIS (BASE);BICINE PH REMARK 280 8.5, 30% V/V PRECIPITANT MIX 1 (20% V/V PEG 500 MME; 10 % W/V REMARK 280 PEG 20000), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 55.90600 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 50 REMARK 465 ILE A 51 REMARK 465 SER A 52 REMARK 465 GLY A 53 REMARK 465 THR A 54 REMARK 465 ALA A 55 REMARK 465 ASP A 56 REMARK 465 GLY A 57 REMARK 465 VAL A 58 REMARK 465 ASN A 59 REMARK 465 GLN A 60 REMARK 465 PRO A 61 REMARK 465 ARG A 62 REMARK 465 HIS A 63 REMARK 465 ASP A 64 REMARK 465 LYS A 65 REMARK 465 VAL A 66 REMARK 465 THR A 67 REMARK 465 THR A 68 REMARK 465 SER A 111 REMARK 465 HIS A 112 REMARK 465 ALA A 113 REMARK 465 VAL A 114 REMARK 465 PRO A 115 REMARK 465 SER A 116 REMARK 465 VAL A 117 REMARK 465 GLY A 118 REMARK 465 ASP A 119 REMARK 465 GLU A 347 REMARK 465 GLU A 348 REMARK 465 ASP A 349 REMARK 465 GLY A 350 REMARK 465 ASP A 351 REMARK 465 THR A 352 REMARK 465 ASP A 353 REMARK 465 ALA A 354 REMARK 465 ILE A 355 REMARK 465 GLN A 356 REMARK 465 PRO A 357 REMARK 465 GLN A 358 REMARK 465 LYS A 359 REMARK 465 HIS A 405 REMARK 465 HIS A 406 REMARK 465 HIS A 407 REMARK 465 HIS A 408 REMARK 465 MET B 50 REMARK 465 ILE B 51 REMARK 465 SER B 52 REMARK 465 GLY B 53 REMARK 465 THR B 54 REMARK 465 ALA B 55 REMARK 465 ASP B 56 REMARK 465 GLY B 57 REMARK 465 VAL B 58 REMARK 465 ASN B 59 REMARK 465 GLN B 60 REMARK 465 PRO B 61 REMARK 465 ARG B 62 REMARK 465 HIS B 63 REMARK 465 ASP B 64 REMARK 465 LYS B 65 REMARK 465 VAL B 66 REMARK 465 THR B 67 REMARK 465 THR B 68 REMARK 465 SER B 111 REMARK 465 HIS B 112 REMARK 465 ALA B 113 REMARK 465 VAL B 114 REMARK 465 PRO B 115 REMARK 465 SER B 116 REMARK 465 VAL B 117 REMARK 465 GLY B 118 REMARK 465 ASP B 119 REMARK 465 GLU B 347 REMARK 465 GLU B 348 REMARK 465 ASP B 349 REMARK 465 GLY B 350 REMARK 465 ASP B 351 REMARK 465 THR B 352 REMARK 465 ASP B 353 REMARK 465 ALA B 354 REMARK 465 ILE B 355 REMARK 465 GLN B 356 REMARK 465 PRO B 357 REMARK 465 GLN B 358 REMARK 465 LYS B 359 REMARK 465 HIS B 405 REMARK 465 HIS B 406 REMARK 465 HIS B 407 REMARK 465 HIS B 408 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 NH1 ARG A 288 O HOH A 601 1.76 REMARK 500 O HOH A 620 O HOH A 704 1.92 REMARK 500 CG2 THR B 193 O HOH A 688 1.98 REMARK 500 OE1 GLU B 386 O HOH B 601 2.00 REMARK 500 O HOH B 829 O HOH B 886 2.02 REMARK 500 O HOH A 613 O HOH A 783 2.03 REMARK 500 O HOH B 601 O HOH B 814 2.06 REMARK 500 O HOH B 806 O HOH B 901 2.08 REMARK 500 O HOH B 722 O HOH B 737 2.11 REMARK 500 O PHE A 147 NH2 ARG A 173 2.11 REMARK 500 O HOH B 685 O HOH B 896 2.12 REMARK 500 NH2 ARG B 221 OD2 ASP B 224 2.12 REMARK 500 O HOH B 740 O HOH B 866 2.16 REMARK 500 O HOH B 866 O HOH B 896 2.19 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 GLU B 183 CD GLU B 183 OE2 0.081 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 MET A 339 CG - SD - CE ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG A 382 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 382 NE - CZ - NH2 ANGL. DEV. = -5.7 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 THR A 162 -57.30 76.64 REMARK 500 HIS A 403 38.06 -86.28 REMARK 500 THR B 175 -120.55 41.07 REMARK 500 ASP B 248 -0.69 76.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 173 0.14 SIDE CHAIN 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 904 DISTANCE = 6.92 ANGSTROMS DBREF 8R44 A 51 402 UNP B4YB07 PHYA2_SOYBN 51 402 DBREF 8R44 B 51 402 UNP B4YB07 PHYA2_SOYBN 51 402 SEQADV 8R44 MET A 50 UNP B4YB07 INITIATING METHIONINE SEQADV 8R44 HIS A 403 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS A 404 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS A 405 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS A 406 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS A 407 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS A 408 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 MET B 50 UNP B4YB07 INITIATING METHIONINE SEQADV 8R44 HIS B 403 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS B 404 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS B 405 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS B 406 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS B 407 UNP B4YB07 EXPRESSION TAG SEQADV 8R44 HIS B 408 UNP B4YB07 EXPRESSION TAG SEQRES 1 A 359 MET ILE SER GLY THR ALA ASP GLY VAL ASN GLN PRO ARG SEQRES 2 A 359 HIS ASP LYS VAL THR THR ALA TYR LEU HIS HIS MET GLN SEQRES 3 A 359 LYS GLY LYS MET ILE GLN PRO PHE GLY CYS LEU LEU ALA SEQRES 4 A 359 LEU ASP GLU LYS THR CYS LYS VAL ILE ALA TYR SER GLU SEQRES 5 A 359 ASN ALA PRO GLU MET LEU THR MET VAL SER HIS ALA VAL SEQRES 6 A 359 PRO SER VAL GLY ASP HIS PRO ALA LEU GLY ILE GLY THR SEQRES 7 A 359 ASP ILE LYS THR LEU PHE THR ALA PRO SER ALA SER ALA SEQRES 8 A 359 LEU GLN LYS ALA LEU GLY PHE ALA GLU VAL LEU LEU LEU SEQRES 9 A 359 ASN PRO VAL LEU ILE HIS CYS LYS THR SER GLY LYS PRO SEQRES 10 A 359 PHE TYR ALA ILE ILE HIS ARG VAL THR GLY SER MET ILE SEQRES 11 A 359 ILE ASP PHE GLU PRO VAL LYS PRO TYR GLU VAL PRO MET SEQRES 12 A 359 THR ALA ALA GLY ALA LEU GLN SER TYR LYS LEU ALA ALA SEQRES 13 A 359 LYS ALA ILE THR ARG LEU GLN SER LEU PRO SER GLY SER SEQRES 14 A 359 MET GLU ARG LEU CYS ASP THR MET VAL GLN GLU VAL PHE SEQRES 15 A 359 GLU LEU THR GLY TYR ASP ARG VAL MET ALA TYR LYS PHE SEQRES 16 A 359 HIS GLU ASP ASP HIS GLY GLU VAL ILE ALA GLU ILE THR SEQRES 17 A 359 LYS PRO GLY LEU GLU PRO TYR LEU GLY LEU HIS TYR PRO SEQRES 18 A 359 ALA THR ASP ILE PRO GLN ALA SER ARG PHE LEU PHE MET SEQRES 19 A 359 LYS ASN LYS VAL ARG MET ILE VAL ASP CYS HIS ALA LYS SEQRES 20 A 359 HIS VAL ARG VAL LEU GLN ASP GLU LYS LEU PRO PHE ASP SEQRES 21 A 359 LEU THR LEU CYS GLY SER THR LEU ARG ALA PRO HIS SER SEQRES 22 A 359 CYS HIS ALA GLN TYR MET ALA ASN MET ASP SER ILE ALA SEQRES 23 A 359 SER LEU VAL MET ALA VAL VAL VAL ASN ASP ASN GLU GLU SEQRES 24 A 359 ASP GLY ASP THR ASP ALA ILE GLN PRO GLN LYS ARG LYS SEQRES 25 A 359 ARG LEU TRP GLY LEU VAL VAL CYS HIS ASN THR THR PRO SEQRES 26 A 359 ARG PHE VAL PRO PHE PRO LEU ARG TYR ALA CYS GLU PHE SEQRES 27 A 359 LEU ALA GLN VAL PHE ALA ILE HIS VAL ASN LYS GLU ILE SEQRES 28 A 359 GLU LEU HIS HIS HIS HIS HIS HIS SEQRES 1 B 359 MET ILE SER GLY THR ALA ASP GLY VAL ASN GLN PRO ARG SEQRES 2 B 359 HIS ASP LYS VAL THR THR ALA TYR LEU HIS HIS MET GLN SEQRES 3 B 359 LYS GLY LYS MET ILE GLN PRO PHE GLY CYS LEU LEU ALA SEQRES 4 B 359 LEU ASP GLU LYS THR CYS LYS VAL ILE ALA TYR SER GLU SEQRES 5 B 359 ASN ALA PRO GLU MET LEU THR MET VAL SER HIS ALA VAL SEQRES 6 B 359 PRO SER VAL GLY ASP HIS PRO ALA LEU GLY ILE GLY THR SEQRES 7 B 359 ASP ILE LYS THR LEU PHE THR ALA PRO SER ALA SER ALA SEQRES 8 B 359 LEU GLN LYS ALA LEU GLY PHE ALA GLU VAL LEU LEU LEU SEQRES 9 B 359 ASN PRO VAL LEU ILE HIS CYS LYS THR SER GLY LYS PRO SEQRES 10 B 359 PHE TYR ALA ILE ILE HIS ARG VAL THR GLY SER MET ILE SEQRES 11 B 359 ILE ASP PHE GLU PRO VAL LYS PRO TYR GLU VAL PRO MET SEQRES 12 B 359 THR ALA ALA GLY ALA LEU GLN SER TYR LYS LEU ALA ALA SEQRES 13 B 359 LYS ALA ILE THR ARG LEU GLN SER LEU PRO SER GLY SER SEQRES 14 B 359 MET GLU ARG LEU CYS ASP THR MET VAL GLN GLU VAL PHE SEQRES 15 B 359 GLU LEU THR GLY TYR ASP ARG VAL MET ALA TYR LYS PHE SEQRES 16 B 359 HIS GLU ASP ASP HIS GLY GLU VAL ILE ALA GLU ILE THR SEQRES 17 B 359 LYS PRO GLY LEU GLU PRO TYR LEU GLY LEU HIS TYR PRO SEQRES 18 B 359 ALA THR ASP ILE PRO GLN ALA SER ARG PHE LEU PHE MET SEQRES 19 B 359 LYS ASN LYS VAL ARG MET ILE VAL ASP CYS HIS ALA LYS SEQRES 20 B 359 HIS VAL ARG VAL LEU GLN ASP GLU LYS LEU PRO PHE ASP SEQRES 21 B 359 LEU THR LEU CYS GLY SER THR LEU ARG ALA PRO HIS SER SEQRES 22 B 359 CYS HIS ALA GLN TYR MET ALA ASN MET ASP SER ILE ALA SEQRES 23 B 359 SER LEU VAL MET ALA VAL VAL VAL ASN ASP ASN GLU GLU SEQRES 24 B 359 ASP GLY ASP THR ASP ALA ILE GLN PRO GLN LYS ARG LYS SEQRES 25 B 359 ARG LEU TRP GLY LEU VAL VAL CYS HIS ASN THR THR PRO SEQRES 26 B 359 ARG PHE VAL PRO PHE PRO LEU ARG TYR ALA CYS GLU PHE SEQRES 27 B 359 LEU ALA GLN VAL PHE ALA ILE HIS VAL ASN LYS GLU ILE SEQRES 28 B 359 GLU LEU HIS HIS HIS HIS HIS HIS HET CYC A 500 43 HET 1PE A 501 16 HET 1PE A 502 16 HET PEG A 503 7 HET PEG A 504 7 HET PGE A 505 10 HET CYC B 500 43 HET 1PE B 501 16 HETNAM CYC PHYCOCYANOBILIN HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 3 CYC 2(C33 H40 N4 O6) FORMUL 4 1PE 3(C10 H22 O6) FORMUL 6 PEG 2(C4 H10 O3) FORMUL 8 PGE C6 H14 O4 FORMUL 11 HOH *587(H2 O) HELIX 1 AA1 TYR A 70 MET A 74 5 5 HELIX 2 AA2 ASN A 102 THR A 108 1 7 HELIX 3 AA3 ASP A 128 LEU A 132 5 5 HELIX 4 AA4 THR A 134 LEU A 145 1 12 HELIX 5 AA5 GLY A 146 PHE A 147 5 2 HELIX 6 AA6 ALA A 148 LEU A 152 5 5 HELIX 7 AA7 LYS A 186 PRO A 191 5 6 HELIX 8 AA8 MET A 192 SER A 213 1 22 HELIX 9 AA9 SER A 218 GLY A 235 1 18 HELIX 10 AB1 PRO A 270 ILE A 274 5 5 HELIX 11 AB2 PRO A 275 ASN A 285 1 11 HELIX 12 AB3 HIS A 321 ASP A 332 1 12 HELIX 13 AB4 PRO A 378 HIS A 403 1 26 HELIX 14 AB5 TYR B 70 GLY B 77 1 8 HELIX 15 AB6 ASN B 102 THR B 108 1 7 HELIX 16 AB7 ASP B 128 LEU B 132 5 5 HELIX 17 AB8 THR B 134 LEU B 145 1 12 HELIX 18 AB9 GLY B 146 PHE B 147 5 2 HELIX 19 AC1 ALA B 148 LEU B 152 5 5 HELIX 20 AC2 LYS B 186 VAL B 190 5 5 HELIX 21 AC3 MET B 192 LEU B 214 1 23 HELIX 22 AC4 SER B 218 GLY B 235 1 18 HELIX 23 AC5 PRO B 270 ILE B 274 5 5 HELIX 24 AC6 PRO B 275 MET B 283 1 9 HELIX 25 AC7 HIS B 321 MET B 331 1 11 HELIX 26 AC8 PRO B 378 HIS B 404 1 27 SHEET 1 AA1 7 MET A 79 ILE A 80 0 SHEET 2 AA1 7 VAL A 298 GLN A 302 -1 O VAL A 298 N ILE A 80 SHEET 3 AA1 7 VAL A 96 SER A 100 -1 N TYR A 99 O LEU A 301 SHEET 4 AA1 7 CYS A 85 ASP A 90 -1 N ALA A 88 O ALA A 98 SHEET 5 AA1 7 SER A 177 PRO A 184 -1 O PHE A 182 N CYS A 85 SHEET 6 AA1 7 PRO A 166 VAL A 174 -1 N TYR A 168 O GLU A 183 SHEET 7 AA1 7 VAL A 156 HIS A 159 -1 N VAL A 156 O ALA A 169 SHEET 1 AA2 6 HIS A 268 TYR A 269 0 SHEET 2 AA2 6 GLY A 250 THR A 257 -1 N GLY A 250 O TYR A 269 SHEET 3 AA2 6 ARG A 238 PHE A 244 -1 N LYS A 243 O GLU A 251 SHEET 4 AA2 6 ARG A 362 ASN A 371 -1 O LEU A 366 N TYR A 242 SHEET 5 AA2 6 ALA A 335 VAL A 343 -1 N LEU A 337 O CYS A 369 SHEET 6 AA2 6 VAL A 287 ILE A 290 -1 N ARG A 288 O VAL A 338 SHEET 1 AA3 7 MET B 79 ILE B 80 0 SHEET 2 AA3 7 VAL B 298 GLN B 302 -1 O VAL B 298 N ILE B 80 SHEET 3 AA3 7 VAL B 96 SER B 100 -1 N TYR B 99 O LEU B 301 SHEET 4 AA3 7 CYS B 85 ASP B 90 -1 N ALA B 88 O ILE B 97 SHEET 5 AA3 7 SER B 177 PRO B 184 -1 O ILE B 180 N LEU B 87 SHEET 6 AA3 7 PRO B 166 VAL B 174 -1 N ILE B 170 O ASP B 181 SHEET 7 AA3 7 VAL B 156 HIS B 159 -1 N VAL B 156 O ALA B 169 SHEET 1 AA4 6 HIS B 268 TYR B 269 0 SHEET 2 AA4 6 GLY B 250 THR B 257 -1 N GLY B 250 O TYR B 269 SHEET 3 AA4 6 ARG B 238 PHE B 244 -1 N LYS B 243 O GLU B 251 SHEET 4 AA4 6 ARG B 362 ASN B 371 -1 O LEU B 366 N TYR B 242 SHEET 5 AA4 6 ALA B 335 VAL B 343 -1 N LEU B 337 O CYS B 369 SHEET 6 AA4 6 VAL B 287 ILE B 290 -1 N ILE B 290 O SER B 336 LINK SG CYS A 323 CAC CYC A 500 1555 1555 1.85 LINK SG CYS B 323 CAC CYC B 500 1555 1555 1.84 CISPEP 1 ASN A 154 PRO A 155 0 -10.43 CISPEP 2 ASN B 154 PRO B 155 0 -10.57 CRYST1 55.287 111.812 68.273 90.00 92.31 90.00 P 1 21 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 0.018087 0.000000 0.000729 0.00000 SCALE2 0.000000 0.008944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014659 0.00000