HEADER PLANT PROTEIN 13-NOV-23 8R45 TITLE PHYTOCHROMOBILIN-ADDUCTED PAS-GAF BIDOMAIN OF GLYCINE MAX PHYTOCHROME TITLE 2 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,P.CHEN,S.NAGANO,J.HUGHES REVDAT 1 08-JAN-25 8R45 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. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 70334 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) : 0.169 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.087 REMARK 3 FREE R VALUE TEST SET COUNT : 3578 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4946 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 250 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4979 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 99 REMARK 3 SOLVENT ATOMS : 465 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50300 REMARK 3 B22 (A**2) : 0.38100 REMARK 3 B33 (A**2) : 0.12400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.584 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5214 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5004 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7069 ; 1.622 ; 1.663 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11547 ; 1.513 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 630 ; 6.740 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ; 9.705 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 883 ;16.205 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 796 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5917 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1111 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 999 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 57 ; 0.228 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2484 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 363 ; 0.151 ; 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): 2532 ; 3.156 ; 2.690 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2532 ; 3.147 ; 2.691 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3155 ; 4.721 ; 4.797 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3156 ; 4.726 ; 4.801 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2682 ; 4.174 ; 3.387 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2683 ; 4.173 ; 3.387 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3913 ; 6.464 ; 5.948 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3914 ; 6.463 ; 5.948 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 67 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1505 14.2120 22.6455 REMARK 3 T TENSOR REMARK 3 T11: 0.0114 T22: 0.0405 REMARK 3 T33: 0.0319 T12: -0.0167 REMARK 3 T13: 0.0027 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.9062 L22: 0.0302 REMARK 3 L33: 0.2515 L12: -0.0385 REMARK 3 L13: -0.1010 L23: 0.0311 REMARK 3 S TENSOR REMARK 3 S11: 0.0561 S12: -0.0721 S13: -0.0771 REMARK 3 S21: -0.0023 S22: -0.0030 S23: -0.0189 REMARK 3 S31: -0.0413 S32: 0.0262 S33: -0.0531 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): 0.8352 1.5620 -6.5903 REMARK 3 T TENSOR REMARK 3 T11: 0.0218 T22: 0.0275 REMARK 3 T33: 0.0356 T12: -0.0175 REMARK 3 T13: 0.0195 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.1040 L22: 0.7522 REMARK 3 L33: 0.3183 L12: -0.1657 REMARK 3 L13: -0.1131 L23: -0.0897 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: 0.0397 S13: -0.0033 REMARK 3 S21: -0.0450 S22: 0.0085 S23: -0.0577 REMARK 3 S31: 0.0298 S32: -0.0754 S33: 0.0027 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 8R45 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_1292134560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-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 : BESSY REMARK 200 BEAMLINE : 14.2 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 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70335 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 42.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 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 (%): 53.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04 M ETHYLENE GLYCOLS (0.01M REMARK 280 DIETHYLENE GLYCOL; 0.01M TRIETHYLENE GLYCOL; 0.01M TETRAETHYLENE REMARK 280 GLYCOL; 0.01M PENTAETHYLENE GLYCOL); 0.1 M TRIS (BASE); BICINE REMARK 280 PH 9.0; 21% PRECIPITANT MIX (7% V/V MPD; 7% PEG 1000; 7% W/V PEG REMARK 280 3350), VAPOR DIFFUSION, HANGING 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 56.26300 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 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 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 ASN A 346 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 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 VAL B 110 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 ASN B 346 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 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 O5 PG4 A 501 O HOH A 601 2.09 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 O HOH A 819 O HOH B 826 1655 1.85 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 A 183 CD GLU A 183 OE1 0.077 REMARK 500 GLU A 220 CD GLU A 220 OE1 -0.076 REMARK 500 GLU B 183 CD GLU B 183 OE1 0.095 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 313 CB - CA - C ANGL. DEV. = -12.5 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 68 42.95 -104.59 REMARK 500 PRO A 121 -179.03 -44.25 REMARK 500 THR A 162 -64.68 84.34 REMARK 500 ASP A 248 -2.94 77.88 REMARK 500 THR B 175 -120.35 38.60 REMARK 500 ASP B 292 103.34 -162.85 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 0.12 SIDE CHAIN REMARK 500 ARG A 288 0.10 SIDE CHAIN REMARK 500 ARG A 362 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8R45 A 51 402 UNP B4YB07 PHYA2_SOYBN 51 402 DBREF 8R45 B 51 402 UNP B4YB07 PHYA2_SOYBN 51 402 SEQADV 8R45 MET A 50 UNP B4YB07 INITIATING METHIONINE SEQADV 8R45 HIS A 403 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS A 404 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS A 405 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS A 406 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS A 407 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS A 408 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 MET B 50 UNP B4YB07 INITIATING METHIONINE SEQADV 8R45 HIS B 403 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS B 404 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS B 405 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS B 406 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 HIS B 407 UNP B4YB07 EXPRESSION TAG SEQADV 8R45 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 O6E A 500 43 HET PG4 A 501 13 HET O6E B 500 43 HETNAM O6E 3-[5-[[(3~{R},4~{R})-3-ETHYL-4-METHYL-5-OXIDANYLIDENE- HETNAM 2 O6E 3,4-DIHYDROPYRROL-2-YL]METHYL]-2-[[5-[(4-ETHYL-3- HETNAM 3 O6E METHYL-5-OXIDANYLIDENE-PYRROL-2-YL)METHYL]-3-(3- HETNAM 4 O6E HYDROXY-3-OXOPROPYL)-4-METHYL-1~{H}-PYRROL-2- HETNAM 5 O6E YL]METHYL]-4-METHYL-1~{H}-PYRROL-3-YL]PROPANOIC ACID HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 3 O6E 2(C33 H38 N4 O6) FORMUL 4 PG4 C8 H18 O5 FORMUL 6 HOH *465(H2 O) HELIX 1 AA1 THR A 68 LYS A 76 1 9 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 LEU A 214 1 23 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 MET A 283 1 9 HELIX 12 AB3 HIS A 321 ASP A 332 1 12 HELIX 13 AB4 PRO A 378 HIS A 406 1 29 HELIX 14 AB5 THR B 68 GLY B 77 1 10 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 ASP B 332 1 12 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 ILE A 97 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 ILE A 158 O PHE A 167 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 MET A 339 O VAL A 367 SHEET 6 AA2 6 VAL A 287 ILE A 290 -1 N ILE A 290 O SER A 336 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 VAL B 174 O SER B 177 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 O6E A 500 1555 1555 1.82 LINK SG CYS B 323 CAC O6E B 500 1555 1555 1.83 CISPEP 1 ASN A 154 PRO A 155 0 -9.92 CISPEP 2 ASN B 154 PRO B 155 0 -8.62 CRYST1 55.542 112.526 68.370 90.00 92.08 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 0.018004 0.000000 0.000653 0.00000 SCALE2 0.000000 0.008887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014636 0.00000