HEADER SIGNALING PROTEIN 12-AUG-20 7JRI TITLE HIGH-RESOLUTION CRYSTAL STRUCTURES OF TRANSIENT INTERMEDIATES IN THE TITLE 2 PHYTOCHROME PHOTOCYCLE, 33 MS STRUCTURE CAVEAT 7JRI RESIDUES LEU A 489 AND VAL A 490 THAT ARE NEXT TO EACH OTHER CAVEAT 2 7JRI IN THE SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE CAVEAT 3 7JRI BETWEEN C AND N IS 2.81. RESIDUES LEU B 246 AND GLU B 247 CAVEAT 4 7JRI THAT ARE NEXT TO EACH OTHER IN THE SAMPLE SEQUENCE ARE NOT CAVEAT 5 7JRI PROPERLY LINKED: DISTANCE BETWEEN C AND N IS 2.18. RESIDUES CAVEAT 6 7JRI LEU B 489 AND VAL B 490 THAT ARE NEXT TO EACH OTHER IN THE CAVEAT 7 7JRI SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE BETWEEN C CAVEAT 8 7JRI AND N IS 2.43. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTORECEPTOR-HISTIDINE KINASE BPHP; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PCM MYXOBACTERIAL PHYTOCHROME; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STIGMATELLA AURANTIACA; SOURCE 3 ORGANISM_TAXID: 41; SOURCE 4 STRAIN: DW4/3-1; SOURCE 5 GENE: STIAU_8420; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS LIGHT PERCEPTION, RED LIGHT RECEPTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHMIDT,E.STOJKOVIC REVDAT 3 18-OCT-23 7JRI 1 REMARK REVDAT 2 14-JUL-21 7JRI 1 JRNL REVDAT 1 07-APR-21 7JRI 0 JRNL AUTH M.CARRILLO,S.PANDEY,J.SANCHEZ,M.NODA,I.POUDYAL,L.ALDAMA, JRNL AUTH 2 T.N.MALLA,E.CLAESSON,W.Y.WAHLGREN,D.FELIZ,V.SRAJER,M.MAJ, JRNL AUTH 3 L.CASTILLON,S.IWATA,E.NANGO,R.TANAKA,T.TANAKA,L.FANGJIA, JRNL AUTH 4 K.TONO,S.OWADA,S.WESTENHOFF,E.A.STOJKOVIC,M.SCHMIDT JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF TRANSIENT JRNL TITL 2 INTERMEDIATES IN THE PHYTOCHROME PHOTOCYCLE. JRNL REF STRUCTURE V. 29 743 2021 JRNL REFN ISSN 0969-2126 JRNL PMID 33756101 JRNL DOI 10.1016/J.STR.2021.03.004 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 3 NUMBER OF REFLECTIONS : 36457 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.294 REMARK 3 R VALUE (WORKING SET) : 0.292 REMARK 3 FREE R VALUE : 0.333 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1792 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2131 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.4510 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.5770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7320 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 95 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.80000 REMARK 3 B22 (A**2) : -0.57000 REMARK 3 B33 (A**2) : -0.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.860 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.393 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.370 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.929 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.900 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7739 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 7364 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10575 ; 2.120 ; 1.680 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16932 ; 1.233 ; 1.590 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 971 ;12.277 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 400 ;33.730 ;19.950 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1179 ;28.073 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 80 ;20.299 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 945 ; 0.210 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8783 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1661 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3878 ; 1.870 ; 2.321 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3877 ; 1.868 ; 2.321 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4848 ; 3.067 ; 3.478 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4849 ; 3.067 ; 3.479 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3861 ; 1.419 ; 2.413 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3862 ; 1.419 ; 2.414 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5727 ; 2.393 ; 3.579 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9272 ; 6.115 ;28.349 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9264 ; 6.118 ;28.376 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7JRI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 41817 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL2 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL2 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.38 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MPCCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68919 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 449.4 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 203.0 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: REFMAC REMARK 200 STARTING MODEL: 6PTQ REMARK 200 REMARK 200 REMARK: PLATES (5 X 5 X 10 UM**3) REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M AMMONIUM ACETATE, 0.085 M REMARK 280 SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 25.5% W/V POLYETHYLENE REMARK 280 GLYCOL 4000, 15% V/V GLYCEROL (CRYO-SCREEN SOLUTION) AND 3 % W/V REMARK 280 BENZAMIDINE HYDROCHLORIDE MIXED WITH 60 MG/ML PROTEIN (3:2) REMARK 280 PROTEIN TO MOTHER LIQUOR RATIO, BATCH MODE, TEMPERATURE 293K 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 41.70000 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 TOTAL BURIED SURFACE AREA: 3520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 THR B 332 OG1 CG2 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 O HOH A 617 O HOH A 646 1.42 REMARK 500 NH1 ARG A 468 O HOH A 601 1.58 REMARK 500 OG SER B 100 O HOH B 701 1.59 REMARK 500 O ASP A 232 O HOH A 602 1.74 REMARK 500 OE2 GLU B 304 O HOH B 702 1.76 REMARK 500 O ALA A 378 O HOH A 603 1.83 REMARK 500 O GLU B 16 NE2 GLN B 196 1.84 REMARK 500 O PHE B 385 NH1 ARG B 415 1.85 REMARK 500 O GLU B 16 OE1 GLN B 196 1.91 REMARK 500 OG SER A 259 O2A 3Q8 A 500 1.98 REMARK 500 OG SER A 100 O HOH A 602 1.98 REMARK 500 O LEU A 152 NH1 ARG A 286 1.99 REMARK 500 O ARG A 306 O HOH A 604 2.00 REMARK 500 OD1 ASP A 147 OG SER A 175 2.02 REMARK 500 O ALA A 45 N ALA A 47 2.03 REMARK 500 O GLU B 16 CD GLN B 196 2.04 REMARK 500 O VAL B 241 O HOH B 703 2.08 REMARK 500 O HOH B 732 O HOH B 740 2.09 REMARK 500 OE1 GLU B 448 CE1 HIS B 455 2.11 REMARK 500 OE1 GLU A 174 O HOH A 605 2.12 REMARK 500 O PRO A 205 NH1 ARG A 207 2.13 REMARK 500 O ALA B 197 CE2 TYR B 201 2.13 REMARK 500 NH2 ARG A 288 OE1 GLU B 123 2.13 REMARK 500 OE1 GLU A 446 O HOH A 606 2.14 REMARK 500 O ALA B 197 CD2 TYR B 201 2.15 REMARK 500 O GLU A 291 OG1 THR A 294 2.15 REMARK 500 OG SER B 259 O1A 3Q8 B 602 2.16 REMARK 500 O HOH B 734 O HOH B 739 2.18 REMARK 500 OE2 GLU B 174 O PHE B 183 2.18 REMARK 500 NE ARG B 239 O HOH B 704 2.19 REMARK 500 O LEU A 345 O ALA A 350 2.19 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 ND1 HIS B 451 O HOH B 702 2444 2.15 REMARK 500 O PRO A 89 O LEU B 72 2555 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 CYS A 13 CB CYS A 13 SG -0.250 REMARK 500 CYS A 13 CB CYS A 13 SG -0.331 REMARK 500 GLU A 107 CD GLU A 107 OE1 -0.089 REMARK 500 GLU A 107 CD GLU A 107 OE2 -0.091 REMARK 500 CYS B 13 CB CYS B 13 SG -0.519 REMARK 500 CYS B 13 CB CYS B 13 SG -0.426 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 PRO A 222 N - CA - CB ANGL. DEV. = -8.2 DEGREES REMARK 500 CYS B 13 N - CA - CB ANGL. DEV. = -15.3 DEGREES REMARK 500 CYS B 13 N - CA - C ANGL. DEV. = 23.2 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 LEU A 10 -131.23 -134.04 REMARK 500 GLN A 12 -10.24 -37.84 REMARK 500 ASP A 14 43.51 -86.86 REMARK 500 ARG A 15 -56.90 -129.66 REMARK 500 GLU A 16 108.26 -34.58 REMARK 500 PRO A 17 87.56 -67.82 REMARK 500 LEU A 20 69.43 -101.34 REMARK 500 PRO A 36 -110.89 -84.54 REMARK 500 ASP A 37 85.20 -24.97 REMARK 500 ARG A 38 114.89 -28.55 REMARK 500 LEU A 40 -176.33 -54.51 REMARK 500 GLU A 41 -97.08 172.07 REMARK 500 ALA A 45 -98.76 25.73 REMARK 500 ASN A 46 16.87 -43.04 REMARK 500 LEU A 51 11.03 -144.08 REMARK 500 GLU A 56 -31.70 -33.38 REMARK 500 GLN A 61 110.77 70.15 REMARK 500 PRO A 62 157.04 -37.75 REMARK 500 ARG A 65 -24.44 154.41 REMARK 500 PRO A 68 151.32 -27.56 REMARK 500 SER A 83 118.20 -161.09 REMARK 500 VAL A 86 109.44 -53.34 REMARK 500 LEU A 88 -169.86 -111.68 REMARK 500 HIS A 98 158.70 173.73 REMARK 500 ASP A 101 50.04 72.21 REMARK 500 GLU A 107 63.06 -118.42 REMARK 500 PRO A 110 -178.04 -52.56 REMARK 500 MET A 117 -48.72 -14.38 REMARK 500 VAL A 129 -44.08 -169.48 REMARK 500 SER A 130 125.32 -27.08 REMARK 500 PRO A 131 29.60 -71.44 REMARK 500 VAL A 135 29.84 -142.77 REMARK 500 ALA A 145 -22.60 -37.73 REMARK 500 PHE A 155 135.57 -21.13 REMARK 500 MET A 159 -66.02 -145.07 REMARK 500 VAL A 160 126.59 70.64 REMARK 500 ASP A 164 169.37 -47.36 REMARK 500 ASP A 166 30.29 -87.11 REMARK 500 TRP A 167 -32.39 73.82 REMARK 500 LEU A 172 -51.46 -22.74 REMARK 500 ALA A 173 -161.90 -120.87 REMARK 500 GLU A 174 177.48 167.47 REMARK 500 SER A 175 87.11 166.01 REMARK 500 ARG A 177 -91.09 -94.05 REMARK 500 LEU A 184 -72.14 -11.30 REMARK 500 PRO A 189 -152.27 -51.81 REMARK 500 ALA A 190 9.54 -162.81 REMARK 500 ASP A 192 -121.53 -32.07 REMARK 500 ILE A 193 88.63 -31.52 REMARK 500 PRO A 194 -137.23 -87.19 REMARK 500 REMARK 500 THIS ENTRY HAS 229 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 64 ARG A 65 -138.84 REMARK 500 ALA A 111 GLU A 112 142.24 REMARK 500 VAL A 135 LYS A 136 146.61 REMARK 500 MET A 186 HIS A 187 -146.60 REMARK 500 LEU A 220 PRO A 221 -46.94 REMARK 500 GLY A 330 GLY A 331 -138.16 REMARK 500 ARG A 404 ALA A 405 120.38 REMARK 500 LEU A 416 ALA A 417 -144.95 REMARK 500 ASP A 478 LEU A 479 149.75 REMARK 500 PRO B 17 ILE B 18 144.00 REMARK 500 GLY B 23 ILE B 24 -145.93 REMARK 500 LEU B 88 PRO B 89 -149.90 REMARK 500 GLU B 109 PRO B 110 -149.32 REMARK 500 LEU B 208 ILE B 209 146.36 REMARK 500 ASN B 251 MET B 252 -149.72 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 A 656 DISTANCE = 6.52 ANGSTROMS DBREF 7JRI A 9 490 UNP Q09E27 Q09E27_STIAD 9 490 DBREF 7JRI B 9 490 UNP Q09E27 Q09E27_STIAD 9 490 SEQRES 1 A 482 ASP LEU SER GLN CYS ASP ARG GLU PRO ILE HIS LEU LEU SEQRES 2 A 482 GLY GLY ILE GLN SER HIS GLY VAL LEU LEU ALA PHE ARG SEQRES 3 A 482 GLY PRO ASP ARG LEU LEU GLU VAL VAL SER ALA ASN ALA SEQRES 4 A 482 GLN ALA LEU LEU GLY ARG PRO PRO GLU THR LEU LEU GLY SEQRES 5 A 482 GLN PRO VAL GLY ARG VAL LEU PRO ALA GLU VAL LEU ALA SEQRES 6 A 482 GLN TRP GLU PRO LEU VAL ALA ARG GLY SER VAL ARG VAL SEQRES 7 A 482 VAL LEU PRO ALA GLY ALA TYR ARG ALA LEU LEU HIS GLU SEQRES 8 A 482 SER ASP GLY LEU THR VAL LEU GLU LEU GLU PRO ALA GLU SEQRES 9 A 482 LEU GLN PRO GLY MET GLU GLU THR ALA LEU GLU VAL VAL SEQRES 10 A 482 ARG ARG LEU VAL SER PRO LEU ALA GLY VAL LYS GLY THR SEQRES 11 A 482 GLN ALA LEU LEU GLN THR ALA ALA ASP THR VAL ARG ALA SEQRES 12 A 482 LEU THR GLY PHE ASP ARG VAL MET VAL TYR ARG PHE ASP SEQRES 13 A 482 ALA ASP TRP HIS GLY GLU VAL LEU ALA GLU SER LYS ARG SEQRES 14 A 482 GLY GLY MET ASP GLY PHE LEU GLY MET HIS PHE PRO ALA SEQRES 15 A 482 THR ASP ILE PRO VAL GLN ALA ARG ALA LEU TYR THR ARG SEQRES 16 A 482 ASN PRO LEU ARG LEU ILE ALA ASP ALA ARG ALA ARG PRO SEQRES 17 A 482 VAL PRO LEU LEU PRO PRO VAL VAL PRO ALA LEU GLY ARG SEQRES 18 A 482 PRO LEU ASP LEU SER ASN SER ALA LEU ARG SER VAL SER SEQRES 19 A 482 PRO VAL HIS LEU GLU TYR LEU ARG ASN MET GLY VAL GLY SEQRES 20 A 482 ALA SER PHE SER LEU SER LEU LEU LYS GLU GLY VAL LEU SEQRES 21 A 482 TRP GLY LEU ILE ALA CYS HIS HIS LEU GLU PRO LEU HIS SEQRES 22 A 482 ILE SER HIS GLU ARG ARG ARG ALA CYS GLU VAL LEU THR SEQRES 23 A 482 GLN LEU LEU ALA LEU GLN LEU SER ALA GLU GLU ARG ALA SEQRES 24 A 482 ALA GLU ALA SER GLU ASP ALA HIS ARG ALA ALA LEU LEU SEQRES 25 A 482 GLY GLN LEU ALA THR ALA MET GLY GLU GLY GLY THR LEU SEQRES 26 A 482 GLU GLU VAL LEU GLU LYS GLU SER GLU ARG VAL LEU ALA SEQRES 27 A 482 LEU THR GLY ALA ALA GLY VAL ALA LEU LEU LEU GLY GLU SEQRES 28 A 482 GLU PRO LEU LEU VAL GLY CYS THR PRO ALA GLN ASP GLU SEQRES 29 A 482 VAL GLU ALA LEU VAL ALA TRP LEU ALA THR GLN PRO PHE SEQRES 30 A 482 GLN THR SER PHE HIS THR ASP ARG LEU GLY THR VAL TYR SEQRES 31 A 482 PRO PRO LEU ALA ALA ARG ALA ASP VAL ALA ALA GLY ILE SEQRES 32 A 482 LEU ALA VAL ARG LEU ALA PRO ALA ALA ALA ARG PHE ALA SEQRES 33 A 482 ILE TRP PHE ARG PRO GLU VAL ALA ARG THR ILE SER TRP SEQRES 34 A 482 ALA GLY ASN PRO ARG LYS PRO ALA GLU PRO GLU PRO GLY SEQRES 35 A 482 HIS GLN ARG LEU HIS PRO ARG GLY SER PHE GLN ALA TRP SEQRES 36 A 482 GLU GLU THR VAL ARG ASP THR SER LEU PRO TRP LYS ARG SEQRES 37 A 482 ALA ASP LEU GLY ALA ALA GLU GLY PHE ARG GLY ALA LEU SEQRES 38 A 482 VAL SEQRES 1 B 482 ASP LEU SER GLN CYS ASP ARG GLU PRO ILE HIS LEU LEU SEQRES 2 B 482 GLY GLY ILE GLN SER HIS GLY VAL LEU LEU ALA PHE ARG SEQRES 3 B 482 GLY PRO ASP ARG LEU LEU GLU VAL VAL SER ALA ASN ALA SEQRES 4 B 482 GLN ALA LEU LEU GLY ARG PRO PRO GLU THR LEU LEU GLY SEQRES 5 B 482 GLN PRO VAL GLY ARG VAL LEU PRO ALA GLU VAL LEU ALA SEQRES 6 B 482 GLN TRP GLU PRO LEU VAL ALA ARG GLY SER VAL ARG VAL SEQRES 7 B 482 VAL LEU PRO ALA GLY ALA TYR ARG ALA LEU LEU HIS GLU SEQRES 8 B 482 SER ASP GLY LEU THR VAL LEU GLU LEU GLU PRO ALA GLU SEQRES 9 B 482 LEU GLN PRO GLY MET GLU GLU THR ALA LEU GLU VAL VAL SEQRES 10 B 482 ARG ARG LEU VAL SER PRO LEU ALA GLY VAL LYS GLY THR SEQRES 11 B 482 GLN ALA LEU LEU GLN THR ALA ALA ASP THR VAL ARG ALA SEQRES 12 B 482 LEU THR GLY PHE ASP ARG VAL MET VAL TYR ARG PHE ASP SEQRES 13 B 482 ALA ASP TRP HIS GLY GLU VAL LEU ALA GLU SER LYS ARG SEQRES 14 B 482 GLY GLY MET ASP GLY PHE LEU GLY MET HIS PHE PRO ALA SEQRES 15 B 482 THR ASP ILE PRO VAL GLN ALA ARG ALA LEU TYR THR ARG SEQRES 16 B 482 ASN PRO LEU ARG LEU ILE ALA ASP ALA ARG ALA ARG PRO SEQRES 17 B 482 VAL PRO LEU LEU PRO PRO VAL VAL PRO ALA LEU GLY ARG SEQRES 18 B 482 PRO LEU ASP LEU SER ASN SER ALA LEU ARG SER VAL SER SEQRES 19 B 482 PRO VAL HIS LEU GLU TYR LEU ARG ASN MET GLY VAL GLY SEQRES 20 B 482 ALA SER PHE SER LEU SER LEU LEU LYS GLU GLY VAL LEU SEQRES 21 B 482 TRP GLY LEU ILE ALA CYS HIS HIS LEU GLU PRO LEU HIS SEQRES 22 B 482 ILE SER HIS GLU ARG ARG ARG ALA CYS GLU VAL LEU THR SEQRES 23 B 482 GLN LEU LEU ALA LEU GLN LEU SER ALA GLU GLU ARG ALA SEQRES 24 B 482 ALA GLU ALA SER GLU ASP ALA HIS ARG ALA ALA LEU LEU SEQRES 25 B 482 GLY GLN LEU ALA THR ALA MET GLY GLU GLY GLY THR LEU SEQRES 26 B 482 GLU GLU VAL LEU GLU LYS GLU SER GLU ARG VAL LEU ALA SEQRES 27 B 482 LEU THR GLY ALA ALA GLY VAL ALA LEU LEU LEU GLY GLU SEQRES 28 B 482 GLU PRO LEU LEU VAL GLY CYS THR PRO ALA GLN ASP GLU SEQRES 29 B 482 VAL GLU ALA LEU VAL ALA TRP LEU ALA THR GLN PRO PHE SEQRES 30 B 482 GLN THR SER PHE HIS THR ASP ARG LEU GLY THR VAL TYR SEQRES 31 B 482 PRO PRO LEU ALA ALA ARG ALA ASP VAL ALA ALA GLY ILE SEQRES 32 B 482 LEU ALA VAL ARG LEU ALA PRO ALA ALA ALA ARG PHE ALA SEQRES 33 B 482 ILE TRP PHE ARG PRO GLU VAL ALA ARG THR ILE SER TRP SEQRES 34 B 482 ALA GLY ASN PRO ARG LYS PRO ALA GLU PRO GLU PRO GLY SEQRES 35 B 482 HIS GLN ARG LEU HIS PRO ARG GLY SER PHE GLN ALA TRP SEQRES 36 B 482 GLU GLU THR VAL ARG ASP THR SER LEU PRO TRP LYS ARG SEQRES 37 B 482 ALA ASP LEU GLY ALA ALA GLU GLY PHE ARG GLY ALA LEU SEQRES 38 B 482 VAL HET 3Q8 A 500 86 HET BEN B 601 9 HET 3Q8 B 602 86 HETNAM 3Q8 3-[2-[[5-[[(3E,4S)-3-ETHYLIDENE-4-METHYL-5- HETNAM 2 3Q8 OXIDANYLIDENE-PYRROL-2-YL]METHYL]-3-(3-HYDROXY-3- HETNAM 3 3Q8 OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-5-[(4- HETNAM 4 3Q8 ETHYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YL)METHYL]-4- HETNAM 5 3Q8 METHYL-1H-PYRROL-3-YL]PROPANOIC ACID HETNAM BEN BENZAMIDINE FORMUL 3 3Q8 2(C33 H40 N4 O6) FORMUL 4 BEN C7 H8 N2 FORMUL 6 HOH *99(H2 O) HELIX 1 AA1 SER A 11 ARG A 15 5 5 HELIX 2 AA2 ASN A 46 LEU A 50 5 5 HELIX 3 AA3 PRO A 54 LEU A 58 5 5 HELIX 4 AA4 PRO A 68 GLN A 74 1 7 HELIX 5 AA5 GLU A 76 ARG A 81 1 6 HELIX 6 AA6 GLY A 116 LEU A 128 1 13 HELIX 7 AA7 THR A 138 GLY A 154 1 17 HELIX 8 AA8 VAL A 195 ASN A 204 1 10 HELIX 9 AA9 LEU A 246 ASN A 251 1 6 HELIX 10 AB1 ARG A 287 GLU A 329 1 43 HELIX 11 AB2 THR A 332 LEU A 345 1 14 HELIX 12 AB3 ALA A 369 ALA A 381 1 13 HELIX 13 AB4 LYS A 475 GLY A 480 1 6 HELIX 14 AB5 SER B 11 GLU B 16 1 6 HELIX 15 AB6 PRO B 55 LEU B 59 5 5 HELIX 16 AB7 PRO B 62 VAL B 66 5 5 HELIX 17 AB8 PRO B 68 GLN B 74 1 7 HELIX 18 AB9 GLN B 74 GLY B 82 1 9 HELIX 19 AC1 GLY B 116 LEU B 128 1 13 HELIX 20 AC2 GLY B 137 GLY B 154 1 18 HELIX 21 AC3 VAL B 195 LEU B 200 1 6 HELIX 22 AC4 SER B 242 GLU B 247 1 6 HELIX 23 AC5 SER B 283 ALA B 298 1 16 HELIX 24 AC6 ALA B 298 ASP B 313 1 16 HELIX 25 AC7 ASP B 313 ALA B 326 1 14 HELIX 26 AC8 MET B 327 GLU B 329 5 3 HELIX 27 AC9 THR B 332 GLU B 340 1 9 HELIX 28 AD1 SER B 341 LEU B 347 1 7 HELIX 29 AD2 ALA B 369 THR B 382 1 14 HELIX 30 AD3 TYR B 398 ALA B 402 5 5 HELIX 31 AD4 ALA B 477 ALA B 488 1 12 SHEET 1 AA1 2 LEU A 31 PHE A 33 0 SHEET 2 AA1 2 THR A 104 LEU A 106 -1 O THR A 104 N PHE A 33 SHEET 1 AA2 2 GLY A 169 GLU A 170 0 SHEET 2 AA2 2 HIS A 187 PHE A 188 -1 N PHE A 188 O GLY A 169 SHEET 1 AA3 2 PHE A 258 SER A 259 0 SHEET 2 AA3 2 ALA A 273 CYS A 274 -1 O CYS A 274 N PHE A 258 SHEET 1 AA4 2 LEU A 262 LYS A 264 0 SHEET 2 AA4 2 VAL A 267 GLY A 270 -1 O VAL A 267 N LYS A 264 SHEET 1 AA5 2 HIS A 390 THR A 391 0 SHEET 2 AA5 2 ILE A 411 LEU A 412 -1 O ILE A 411 N THR A 391 SHEET 1 AA6 2 ARG A 433 ALA A 438 0 SHEET 2 AA6 2 ALA A 462 VAL A 467 -1 O TRP A 463 N TRP A 437 SHEET 1 AA7 3 TYR B 161 PHE B 163 0 SHEET 2 AA7 3 GLY B 169 VAL B 171 -1 O GLU B 170 N ARG B 162 SHEET 3 AA7 3 GLY B 185 PHE B 188 -1 O GLY B 185 N VAL B 171 SHEET 1 AA8 2 LEU B 206 ILE B 209 0 SHEET 2 AA8 2 SER B 257 LEU B 260 -1 O SER B 257 N ILE B 209 SHEET 1 AA9 2 GLY B 352 LEU B 355 0 SHEET 2 AA9 2 ALA B 424 PHE B 427 -1 O PHE B 427 N GLY B 352 SHEET 1 AB1 2 SER B 388 PHE B 389 0 SHEET 2 AB1 2 ALA B 413 VAL B 414 -1 O ALA B 413 N PHE B 389 SHEET 1 AB2 2 GLU B 446 PRO B 447 0 SHEET 2 AB2 2 LEU B 454 HIS B 455 -1 O HIS B 455 N GLU B 446 LINK SG ACYS A 13 CBCA3Q8 A 500 1555 1555 1.86 LINK SG BCYS A 13 CBCB3Q8 A 500 1555 1555 1.86 LINK SG ACYS B 13 CBCA3Q8 B 602 1555 1555 1.83 LINK SG BCYS B 13 CBCB3Q8 B 602 1555 1555 1.86 CISPEP 1 LEU B 220 PRO B 221 0 -0.76 CRYST1 83.690 83.400 86.870 90.00 107.63 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 0.011949 0.000000 0.003797 0.00000 SCALE2 0.000000 0.011990 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012079 0.00000