HEADER SIGNALING PROTEIN 02-OCT-14 4WKK OBSLTE 20-JAN-16 4WKK 5I5L TITLE THE PHOTOSENSORY MODULE (PAS-GAF-PHY) OF THE BACTERIAL PHYTOCHROME TITLE 2 AGP1 (ATBPHP1) IN THE PR FORM, CHROMOPHORE MODELLED WITH AN EXOCYCLIC TITLE 3 DOUBLE BOND AT PYRROLE RING A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOPHYTOCHROME PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-495; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: THE RESIDUE NUMBERING IN THE PDB ENTRY DIFFERS FROM COMPND 8 THE ONE SHOWN IN THIS SEQUENCE ALIGNMENT. THE FIRST RESIDUE IN THE COMPND 9 PDB ENTRY IS 'LEU17' IN ACCORDANCE WITH THE SEQUENCE FOR THE ENTRY COMPND 10 AAT99575 (NCBI). THE RESPECTIVE NUMBERING WAS USED IN A NUMBER OF COMPND 11 PUBLICATIONS ON THIS PROTEIN, AND WE DID NOT CHANGE IT IN THIS ENTRY COMPND 12 FOR THE SAKE OF CONSISTENCY WITH PUBLISHED WORK AND BECAUSE THE TRUE COMPND 13 N-TERMINUS HAS NOT YET BEEN IDENTIFIED AT THE PROTEIN LEVEL. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 176299; SOURCE 4 STRAIN: C58 / ATCC 33970; SOURCE 5 GENE: ATU1990; 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: PET21B(+) KEYWDS SIGNALING PROTEIN, SURFACE MUTATIONS, BILIN CHROMOPHORE, KEYWDS 2 PHOTOISOMERIZATION EXPDTA X-RAY DIFFRACTION AUTHOR S.NAGANO,P.SCHEERER,K.ZUBOW,T.LAMPARTER,N.KRAUSS REVDAT 4 08-NOV-23 4WKK 1 OBSLTE REVDAT 3 23-JUN-21 4WKK 1 OBSLTE LINK REVDAT 2 20-JAN-16 4WKK 1 REVDAT 1 23-DEC-15 4WKK 0 JRNL AUTH S.NAGANO,P.SCHEERER,K.ZUBOW,N.MICHAEL,K.INOMATA,T.LAMPARTER, JRNL AUTH 2 N.KRAUSS JRNL TITL THE PHOTOSENSORY MODULE (PAS-GAF-PHY) OF THE BACTERIAL JRNL TITL 2 PHYTOCHROME AGP1 (ATBPHP1) IN THE PR FORM, CHROMOPHORE JRNL TITL 3 MODELLED WITH AN EXOCYCLIC DOUBLE BOND IN PYRROLE RING A. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 46971 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2527 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3447 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 189 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 347 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.501 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3980 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3813 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5434 ; 1.534 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8772 ; 0.917 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 525 ; 5.795 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;34.984 ;23.491 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 652 ;14.119 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;15.359 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4582 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 914 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 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 17 A 311 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2851 -24.5145 9.0551 REMARK 3 T TENSOR REMARK 3 T11: 0.0857 T22: 0.0798 REMARK 3 T33: 0.0753 T12: -0.0313 REMARK 3 T13: -0.0022 T23: 0.0677 REMARK 3 L TENSOR REMARK 3 L11: 0.7939 L22: 0.8658 REMARK 3 L33: 1.2404 L12: -0.2824 REMARK 3 L13: 0.4822 L23: 0.0757 REMARK 3 S TENSOR REMARK 3 S11: -0.1417 S12: 0.1203 S13: 0.1015 REMARK 3 S21: 0.1703 S22: 0.0050 S23: 0.0729 REMARK 3 S31: -0.1618 S32: 0.1061 S33: 0.1367 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 312 A 504 REMARK 3 ORIGIN FOR THE GROUP (A): 22.7774 -32.3833 -28.7344 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.0619 REMARK 3 T33: 0.0412 T12: -0.0184 REMARK 3 T13: -0.0122 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 1.1062 L22: 0.4381 REMARK 3 L33: 0.9484 L12: -0.6934 REMARK 3 L13: -0.4942 L23: 0.3553 REMARK 3 S TENSOR REMARK 3 S11: 0.1079 S12: 0.0458 S13: 0.0162 REMARK 3 S21: -0.0729 S22: -0.0195 S23: -0.0108 REMARK 3 S31: -0.0770 S32: 0.0997 S33: -0.0884 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 601 A 604 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8635 -22.3340 -1.6848 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.2330 REMARK 3 T33: 0.2138 T12: -0.0571 REMARK 3 T13: -0.0328 T23: 0.0877 REMARK 3 L TENSOR REMARK 3 L11: 3.4641 L22: 0.2952 REMARK 3 L33: 3.8706 L12: -0.2911 REMARK 3 L13: 0.4092 L23: -1.0486 REMARK 3 S TENSOR REMARK 3 S11: -0.2295 S12: 0.1695 S13: -0.0088 REMARK 3 S21: 0.0810 S22: -0.0131 S23: -0.0471 REMARK 3 S31: -0.2426 S32: 0.0299 S33: 0.2427 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 701 A 1047 REMARK 3 ORIGIN FOR THE GROUP (A): 15.7753 -29.0230 -7.5299 REMARK 3 T TENSOR REMARK 3 T11: 0.0684 T22: 0.1398 REMARK 3 T33: 0.1253 T12: -0.0425 REMARK 3 T13: -0.0270 T23: 0.0624 REMARK 3 L TENSOR REMARK 3 L11: 0.1419 L22: 0.4228 REMARK 3 L33: 0.7359 L12: -0.1771 REMARK 3 L13: -0.0079 L23: 0.2573 REMARK 3 S TENSOR REMARK 3 S11: -0.0018 S12: 0.0623 S13: -0.0295 REMARK 3 S21: 0.0248 S22: -0.0167 S23: 0.0372 REMARK 3 S31: -0.0699 S32: 0.0524 S33: 0.0185 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 4WKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 OBSOLETION UPON AUTHORS REQUEST, NO KNOWN SUPERSEDING ENTRY REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000202896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0718 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 34.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2O9C, 2VEA (PHY DOMAIN ONLY) REMARK 200 REMARK 200 REMARK: BIPYRAMIDAL. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03 M DIETHYLENEGLYCOL, 0.03 M REMARK 280 TRIETHYLENEGLYCOL, 0.03 M TETRAETHYLENEGLYCOL, 0.03 M REMARK 280 PENTAETHYLENEGLYCOL, 20% GLYCEROL, 10% PEG8000, 0.05 M MES, 0.05 REMARK 280 M IMIDAZOLE PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 118.41950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.67400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.67400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 177.62925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.67400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.67400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.20975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.67400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.67400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 177.62925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.67400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.67400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.20975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 118.41950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 69.34800 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -69.34800 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 757 LIES ON A SPECIAL POSITION. 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 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 HIS A 13 REMARK 465 THR A 14 REMARK 465 PRO A 15 REMARK 465 LYS A 16 REMARK 465 LEU A 505 REMARK 465 GLU A 506 REMARK 465 HIS A 507 REMARK 465 HIS A 508 REMARK 465 HIS A 509 REMARK 465 HIS A 510 REMARK 465 HIS A 511 REMARK 465 HIS A 512 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 ARG A 43 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 VAL A 60 CG1 CG2 REMARK 470 GLU A 392 CG CD OE1 OE2 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 ARG A 43 -78.49 -50.35 REMARK 500 SER A 139 -67.75 -96.75 REMARK 500 ALA A 140 82.53 50.84 REMARK 500 GLU A 390 31.42 -90.34 REMARK 500 GLU A 392 104.89 63.59 REMARK 500 ASP A 395 -62.63 -139.83 REMARK 500 ALA A 416 58.29 -145.63 REMARK 500 SER A 425 -177.61 78.98 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 954 DISTANCE = 6.46 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD1 REMARK 620 2 PHE A 168 O 79.5 REMARK 620 3 HOH A 931 O 90.9 80.3 REMARK 620 4 HOH A1022 O 144.3 65.6 90.3 REMARK 620 5 HOH A1034 O 132.7 135.6 120.7 75.0 REMARK 620 6 HOH A1035 O 75.2 149.5 83.4 140.3 74.9 REMARK 620 7 HOH A1036 O 81.3 75.7 155.8 83.2 80.1 116.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3Q8 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WKL RELATED DB: PDB REMARK 900 THE OTHER ENTRY WITH THE DEPOSITION PDB 4WKL PRESENTS A STRUCTURE REMARK 900 WITH AN ALTERNATIVE INTERPRETATION OF THE GEOMETRY OF THE LIGAND. REMARK 900 BOTH THE PRESENT AND 4WKL STRUCTURES HAVE BEEN MODELLED USING THE REMARK 900 SAME DIFFRACTION DATASET. DBREF 4WKK A 10 504 UNP Q7CY45 Q7CY45_AGRT5 1 495 SEQADV 4WKK ALA A 86 UNP Q7CY45 GLU 77 ENGINEERED MUTATION SEQADV 4WKK ALA A 87 UNP Q7CY45 GLU 78 ENGINEERED MUTATION SEQADV 4WKK ALA A 336 UNP Q7CY45 GLU 327 ENGINEERED MUTATION SEQADV 4WKK ALA A 337 UNP Q7CY45 LYS 328 ENGINEERED MUTATION SEQADV 4WKK LEU A 505 UNP Q7CY45 EXPRESSION TAG SEQADV 4WKK GLU A 506 UNP Q7CY45 EXPRESSION TAG SEQADV 4WKK HIS A 507 UNP Q7CY45 EXPRESSION TAG SEQADV 4WKK HIS A 508 UNP Q7CY45 EXPRESSION TAG SEQADV 4WKK HIS A 509 UNP Q7CY45 EXPRESSION TAG SEQADV 4WKK HIS A 510 UNP Q7CY45 EXPRESSION TAG SEQADV 4WKK HIS A 511 UNP Q7CY45 EXPRESSION TAG SEQADV 4WKK HIS A 512 UNP Q7CY45 EXPRESSION TAG SEQRES 1 A 503 MET SER SER HIS THR PRO LYS LEU ASP SER CYS GLY ALA SEQRES 2 A 503 GLU PRO ILE HIS ILE PRO GLY ALA ILE GLN GLU HIS GLY SEQRES 3 A 503 ALA LEU LEU VAL LEU SER ALA ARG GLU PHE SER VAL VAL SEQRES 4 A 503 GLN ALA SER ASP ASN LEU ALA ASN TYR ILE GLY VAL ASP SEQRES 5 A 503 LEU PRO ILE GLY ALA VAL ALA THR GLU ALA ASN LEU PRO SEQRES 6 A 503 PHE ILE SER VAL LEU SER ALA TRP TYR SER GLY ALA ALA SEQRES 7 A 503 SER ASN PHE ARG TYR ALA TRP ALA GLU LYS LYS LEU ASP SEQRES 8 A 503 VAL SER ALA HIS ARG SER GLY THR LEU VAL ILE LEU GLU SEQRES 9 A 503 VAL GLU LYS ALA GLY VAL GLY GLU SER ALA GLU LYS LEU SEQRES 10 A 503 MET GLY GLU LEU THR SER LEU ALA LYS TYR LEU ASN SER SEQRES 11 A 503 ALA PRO SER LEU GLU ASP ALA LEU PHE ARG THR ALA GLN SEQRES 12 A 503 LEU VAL SER SER ILE SER GLY HIS ASP ARG THR LEU ILE SEQRES 13 A 503 TYR ASP PHE GLY LEU ASP TRP SER GLY HIS VAL VAL ALA SEQRES 14 A 503 GLU ALA GLY SER GLY ALA LEU PRO SER TYR LEU GLY LEU SEQRES 15 A 503 ARG PHE PRO ALA GLY ASP ILE PRO PRO GLN ALA ARG GLN SEQRES 16 A 503 LEU TYR THR ILE ASN ARG LEU ARG MET ILE PRO ASP VAL SEQRES 17 A 503 ASP TYR LYS PRO VAL PRO ILE ARG PRO GLU VAL ASN ALA SEQRES 18 A 503 GLU THR GLY ALA VAL LEU ASP MET SER PHE SER GLN LEU SEQRES 19 A 503 ARG SER VAL SER PRO VAL HIS LEU GLU TYR MET ARG ASN SEQRES 20 A 503 MET GLY THR ALA ALA SER MET SER VAL SER ILE VAL VAL SEQRES 21 A 503 ASN GLY ALA LEU TRP GLY LEU ILE ALA CYS HIS HIS ALA SEQRES 22 A 503 THR PRO HIS SER VAL SER LEU ALA VAL ARG GLU ALA CYS SEQRES 23 A 503 ASP PHE ALA ALA GLN LEU LEU SER MET ARG ILE ALA MET SEQRES 24 A 503 GLU GLN SER SER GLN ASP ALA SER ARG ARG VAL GLU LEU SEQRES 25 A 503 GLY HIS ILE GLN ALA ARG LEU LEU LYS GLY MET ALA ALA SEQRES 26 A 503 ALA ALA ALA TRP VAL ASP GLY LEU LEU GLY GLY GLU GLY SEQRES 27 A 503 GLU ARG GLU ASP LEU LEU LYS GLN VAL GLY ALA ASP GLY SEQRES 28 A 503 ALA ALA LEU VAL LEU GLY ASP ASP TYR GLU LEU VAL GLY SEQRES 29 A 503 ASN THR PRO SER ARG GLU GLN VAL GLU GLU LEU ILE LEU SEQRES 30 A 503 TRP LEU GLY GLU ARG GLU ILE ALA ASP VAL PHE ALA THR SEQRES 31 A 503 ASP ASN LEU ALA GLY ASN TYR PRO THR ALA ALA ALA TYR SEQRES 32 A 503 ALA SER VAL ALA SER GLY ILE ILE ALA MET ARG VAL SER SEQRES 33 A 503 GLU LEU HIS GLY SER TRP LEU ILE TRP PHE ARG PRO GLU SEQRES 34 A 503 VAL ILE LYS THR VAL ARG TRP GLY GLY ASP PRO HIS LYS SEQRES 35 A 503 THR VAL GLN GLU SER GLY ARG ILE HIS PRO ARG LYS SER SEQRES 36 A 503 PHE GLU ILE TRP LYS GLU GLN LEU ARG ASN THR SER PHE SEQRES 37 A 503 PRO TRP SER GLU PRO GLU LEU ALA ALA ALA ARG GLU LEU SEQRES 38 A 503 ARG GLY ALA ILE ILE GLY ILE VAL LEU ARG LYS THR GLU SEQRES 39 A 503 GLU LEU GLU HIS HIS HIS HIS HIS HIS HET 3Q8 A 601 43 HET CA A 602 1 HET GOL A 603 6 HET IMD A 604 5 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 CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM IMD IMIDAZOLE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 3Q8 C33 H40 N4 O6 FORMUL 3 CA CA 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 IMD C3 H5 N2 1+ FORMUL 6 HOH *347(H2 O) HELIX 1 AA1 ASP A 18 GLU A 23 1 6 HELIX 2 AA2 ASN A 53 GLY A 59 1 7 HELIX 3 AA3 PHE A 75 SER A 84 1 10 HELIX 4 AA4 ALA A 95 LYS A 97 5 3 HELIX 5 AA5 SER A 122 ASN A 138 1 17 HELIX 6 AA6 SER A 142 GLY A 159 1 18 HELIX 7 AA7 PRO A 194 ILE A 198 5 5 HELIX 8 AA8 PRO A 199 ASN A 209 1 11 HELIX 9 AA9 SER A 247 GLY A 258 1 12 HELIX 10 AB1 SER A 288 ALA A 335 1 48 HELIX 11 AB2 VAL A 339 GLY A 344 1 6 HELIX 12 AB3 GLY A 345 GLN A 355 1 11 HELIX 13 AB4 SER A 377 GLU A 390 1 14 HELIX 14 AB5 ASN A 401 TYR A 406 1 6 HELIX 15 AB6 PRO A 407 ALA A 411 5 5 HELIX 16 AB7 TYR A 412 SER A 417 1 6 HELIX 17 AB8 SER A 480 GLU A 503 1 24 SHEET 1 AA1 7 ALA A 30 ILE A 31 0 SHEET 2 AA1 7 VAL A 222 ARG A 225 -1 O VAL A 222 N ILE A 31 SHEET 3 AA1 7 VAL A 47 SER A 51 -1 N ALA A 50 O ARG A 225 SHEET 4 AA1 7 GLY A 35 SER A 41 -1 N VAL A 39 O VAL A 48 SHEET 5 AA1 7 LEU A 109 LYS A 116 -1 O LEU A 112 N LEU A 38 SHEET 6 AA1 7 LEU A 99 SER A 106 -1 N SER A 102 O GLU A 113 SHEET 7 AA1 7 ASN A 89 TRP A 94 -1 N TYR A 92 O VAL A 101 SHEET 1 AA2 6 ARG A 192 PHE A 193 0 SHEET 2 AA2 6 GLY A 174 GLY A 181 -1 N GLY A 174 O PHE A 193 SHEET 3 AA2 6 ARG A 162 PHE A 168 -1 N ASP A 167 O HIS A 175 SHEET 4 AA2 6 ALA A 272 HIS A 281 -1 O LEU A 276 N TYR A 166 SHEET 5 AA2 6 ALA A 261 VAL A 269 -1 N MET A 263 O CYS A 279 SHEET 6 AA2 6 LEU A 211 ILE A 214 -1 N ILE A 214 O SER A 262 SHEET 1 AA3 5 ASP A 368 GLY A 373 0 SHEET 2 AA3 5 GLY A 360 LEU A 365 -1 N ALA A 361 O VAL A 372 SHEET 3 AA3 5 TRP A 431 ARG A 436 -1 O TRP A 431 N VAL A 364 SHEET 4 AA3 5 GLY A 418 ARG A 423 -1 N MET A 422 O LEU A 432 SHEET 5 AA3 5 PHE A 397 THR A 399 -1 N PHE A 397 O ALA A 421 SHEET 1 AA4 2 LYS A 441 GLY A 446 0 SHEET 2 AA4 2 ILE A 467 LEU A 472 -1 O LEU A 472 N LYS A 441 SHEET 1 AA5 2 THR A 452 GLU A 455 0 SHEET 2 AA5 2 ARG A 458 PRO A 461 -1 O HIS A 460 N VAL A 453 LINK SG CYS A 20 CBC 3Q8 A 601 1555 1555 1.82 LINK OD1 ASP A 167 CA CA A 602 1555 1555 2.45 LINK O PHE A 168 CA CA A 602 1555 1555 2.37 LINK CA CA A 602 O HOH A 931 1555 1555 2.62 LINK CA CA A 602 O HOH A1022 1555 1555 2.58 LINK CA CA A 602 O HOH A1034 1555 1555 2.37 LINK CA CA A 602 O HOH A1035 1555 1555 2.60 LINK CA CA A 602 O HOH A1036 1555 1555 2.28 CISPEP 1 ARG A 225 PRO A 226 0 -4.94 CISPEP 2 ARG A 225 PRO A 226 0 -7.76 SITE 1 AC1 24 CYS A 20 TYR A 166 TYR A 188 PHE A 193 SITE 2 AC1 24 GLY A 196 ASP A 197 ILE A 198 PRO A 199 SITE 3 AC1 24 TYR A 206 ARG A 244 VAL A 246 SER A 247 SITE 4 AC1 24 VAL A 249 HIS A 250 TYR A 253 SER A 262 SITE 5 AC1 24 SER A 264 HIS A 280 ILE A 459 HOH A 809 SITE 6 AC1 24 HOH A 812 HOH A 840 HOH A 928 HOH A 929 SITE 1 AC2 7 ASP A 167 PHE A 168 HOH A 931 HOH A1022 SITE 2 AC2 7 HOH A1034 HOH A1035 HOH A1036 SITE 1 AC3 8 ASP A 161 ARG A 162 GLY A 181 SER A 182 SITE 2 AC3 8 GLY A 183 ALA A 184 LEU A 185 PRO A 186 SITE 1 AC4 5 GLN A 32 ARG A 212 MET A 213 GLN A 242 SITE 2 AC4 5 ARG A 244 CRYST1 69.348 69.348 236.839 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014420 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004222 0.00000